ERROR [2017-03-07 12:24:44,307] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,308] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,468] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,469] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,628] [ZoomDataBlock.java:111] Error reading Zoom level 3 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,629] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,781] [ZoomDataBlock.java:111] Error reading Zoom level 3 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,782] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,924] [ZoomDataBlock.java:111] Error reading Zoom level 4 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:44,925] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:45,084] [ZoomDataBlock.java:111] Error reading Zoom level 4 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:45,084] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:45,988] [ZoomDataBlock.java:111] Error reading Zoom level 3 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:45,988] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,158] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,159] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,292] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,292] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,444] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,444] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,579] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,580] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,730] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,731] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,902] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,903] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,920] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:46,921] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,330] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,331] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,346] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,347] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,363] [ZoomDataBlock.java:111] Error reading Zoom level 2 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,364] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,380] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,380] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,397] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,398] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,413] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,414] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,430] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,431] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,447] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,448] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,464] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,465] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,481] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,481] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,498] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,498] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,581] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,582] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,599] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,599] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,616] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,617] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,631] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,632] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,649] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,650] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,667] [ZoomDataBlock.java:111] Error reading Zoom level 1 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:47,668] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:50,892] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:50,893] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:52,528] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:52,537] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:52,727] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:52,727] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.loadScores(DataTrack.java:215) at org.broad.igv.track.DataTrack.getInViewScores(DataTrack.java:131) at org.broad.igv.track.DataTrack.getInViewRange(DataTrack.java:159) at org.broad.igv.ui.panel.DataPanelContainer.autoscaleGroup(DataPanelContainer.java:312) at org.broad.igv.ui.panel.DataPanelContainer.autoscale(DataPanelContainer.java:285) at org.broad.igv.ui.panel.DataPanelContainer.paintChildren(DataPanelContainer.java:153) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JViewport.paint(JViewport.java:728) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JLayeredPane.paint(JLayeredPane.java:586) at javax.swing.JComponent.paintChildren(JComponent.java:889) at javax.swing.JComponent.paint(JComponent.java:1065) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,322] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,323] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,337] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,338] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,353] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,354] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,371] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,371] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,387] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,388] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,469] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,470] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,509] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,510] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,565] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,566] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,583] [ZoomDataBlock.java:111] Error reading Zoom level 5 data for leaf item java.io.EOFException at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:63) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:101) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-07 12:24:54,584] [DefaultExceptionHandler.java:49] Unhandled exception java.util.MissingFormatArgumentException: Format specifier '%d' at java.util.Formatter.format(Formatter.java:2519) at java.util.Formatter.format(Formatter.java:2455) at java.lang.String.format(String.java:2940) at org.broad.igv.bbfile.ZoomDataBlock.(ZoomDataBlock.java:112) at org.broad.igv.bbfile.ZoomLevelIterator.getDataBlock(ZoomLevelIterator.java:392) at org.broad.igv.bbfile.ZoomLevelIterator.getHitRegion(ZoomLevelIterator.java:314) at org.broad.igv.bbfile.ZoomLevelIterator.(ZoomLevelIterator.java:105) at org.broad.igv.bbfile.BBFileReader.getZoomLevelIterator(BBFileReader.java:420) at org.broad.igv.bigwig.BigWigDataSource.getZoomSummaryScores(BigWigDataSource.java:247) at org.broad.igv.bigwig.BigWigDataSource.getPrecomputedSummaryScores(BigWigDataSource.java:191) at org.broad.igv.data.AbstractDataSource.getSummaryScoresForRange(AbstractDataSource.java:143) at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:121) at org.broad.igv.track.DataTrack.getLocusScoreAt(DataTrack.java:285) at org.broad.igv.track.DataTrack.getValueStringAt(DataTrack.java:268) at org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:437) at org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:580) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6578) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6302) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-03-07 12:24:55,833] [ShutdownThread.java:51] Shutting down INFO [2017-03-07 12:24:57,956] [Main.java:134] Startup IGV Version 2.3.89 (142)12/22/2016 01:32 PM INFO [2017-03-07 12:24:57,957] [Main.java:135] Java 1.8.0_111 INFO [2017-03-07 12:24:57,957] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-07 12:24:58,578] [Main.java:136] Default User Directory: /Users/morova INFO [2017-03-07 12:24:58,579] [Main.java:137] OS: Mac OS X INFO [2017-03-07 12:25:02,723] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-07 12:25:06,209] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-07 12:25:06,293] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-07 12:25:13,214] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/LNCAP_Marks/LNCaP_DNAseI/ENCFF001UWU.bed.gz ERROR [2017-03-07 12:25:15,470] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 12:25:33,561] [ShutdownThread.java:51] Shutting down INFO [2017-03-07 12:32:29,593] [Main.java:134] Startup IGV Version 2.3.89 (142)12/22/2016 01:32 PM INFO [2017-03-07 12:32:29,594] [Main.java:135] Java 1.8.0_111 INFO [2017-03-07 12:32:29,595] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-07 12:32:30,340] [Main.java:136] Default User Directory: /Users/morova INFO [2017-03-07 12:32:30,341] [Main.java:137] OS: Mac OS X INFO [2017-03-07 12:32:34,186] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-07 12:32:37,231] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-07 12:32:37,308] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-07 12:32:43,898] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/epithelial_cell_of_prostate/Dnaseq/rawdata/prostate_EC_hg19.bed ERROR [2017-03-07 12:32:44,365] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 12:32:57,709] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/epithelial_cell_of_prostate/Dnaseq/rawdata/prostate_EC_overlap_grch37.bed ERROR [2017-03-07 12:32:58,450] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 12:37:31,687] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/Dnaseq_vs_ARsites/DNaseq_bed/prostate_EC_overlap_grch37.bed ERROR [2017-03-07 12:37:31,888] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 12:37:41,227] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/Dnaseq_vs_ARsites/DNaseq_bed/labeled_merged_sorted_prostate_overlap_250.bed ERROR [2017-03-07 12:37:41,650] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 12:44:08,477] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/epithelial_cell_of_prostate/Dnaseq/rawdata/prostate_EC_hg19.narrowpeak ERROR [2017-03-07 12:44:08,906] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 12:44:11,388] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/epithelial_cell_of_prostate/Dnaseq/rawdata/prostate_EC_hg19.bed ERROR [2017-03-07 12:44:11,547] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 12:50:24,005] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/epithelial_cell_of_prostate/Dnaseq/rawdata/prostate_EC_hg19.bed ERROR [2017-03-07 12:50:25,618] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 16:16:04,615] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/LNCAP_DNAseq_AR_sites/bed/LNCaP_DNAse_grch37_250.bed ERROR [2017-03-07 16:16:05,840] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-07 16:16:52,028] [ShutdownThread.java:51] Shutting down INFO [2017-03-13 12:26:07,495] [Main.java:134] Startup IGV Version 2.3.89 (142)12/22/2016 01:32 PM INFO [2017-03-13 12:26:07,496] [Main.java:135] Java 1.8.0_111 INFO [2017-03-13 12:26:07,496] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-13 12:26:08,870] [Main.java:136] Default User Directory: /Users/morova INFO [2017-03-13 12:26:08,871] [Main.java:137] OS: Mac OS X INFO [2017-03-13 12:26:16,058] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-13 12:26:20,334] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-13 12:26:20,447] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-13 12:26:35,347] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/lncap_high_conf_comparison/GSE83860_ChIPseq_LNCaP_AR_DHT.bw ERROR [2017-03-13 12:26:35,534] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-13 12:26:48,645] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/lncap_high_conf_comparison/GSE83860_ChIPseq_LNCaP_AR_DHT.bedgraph ERROR [2017-03-13 12:26:48,794] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-13 12:26:53,612] [ShutdownThread.java:51] Shutting down INFO [2017-03-13 13:03:04,188] [Main.java:134] Startup IGV Version 2.3.89 (142)12/22/2016 01:32 PM INFO [2017-03-13 13:03:04,189] [Main.java:135] Java 1.8.0_111 INFO [2017-03-13 13:03:04,189] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-13 13:03:04,997] [Main.java:136] Default User Directory: /Users/morova INFO [2017-03-13 13:03:04,997] [Main.java:137] OS: Mac OS X INFO [2017-03-13 13:03:09,006] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-13 13:03:12,120] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-13 13:03:12,213] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-13 13:03:25,723] [TrackLoader.java:126] Loading resource, path /Users/morova/closed_chromatin.bed ERROR [2017-03-13 13:03:26,068] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-13 13:03:57,232] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/Dnaseq_vs_ARsites/DNaseq_bed/labeled_merged_sorted_prostate_overlap_250.bed ERROR [2017-03-13 13:03:57,635] [DataPanelContainer.java:232] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-13 13:05:42,095] [ShutdownThread.java:51] Shutting down INFO [2017-03-15 09:55:57,508] [Main.java:135] Startup IGV Version 2.3.91 (145)02/07/2017 03:38 PM INFO [2017-03-15 09:55:57,509] [Main.java:136] Java 1.8.0_121 INFO [2017-03-15 09:55:57,509] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-15 09:55:57,515] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-15 09:55:57,515] [Main.java:138] OS: Mac OS X INFO [2017-03-15 09:55:59,296] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-15 09:56:01,748] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-15 09:56:01,825] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-15 09:58:24,847] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF522NXN.bed ERROR [2017-03-15 09:58:26,154] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-15 10:00:53,152] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF687NGB.bed.gz INFO [2017-03-15 10:00:54,137] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF728FBW.bed.gz ERROR [2017-03-15 10:00:54,804] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-15 10:06:34,037] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF687NGB.bed.gz INFO [2017-03-15 10:06:34,707] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF728FBW.bed.gz INFO [2017-03-15 10:06:35,484] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF522NXN.bed.gz ERROR [2017-03-15 10:06:36,240] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-15 17:52:15,171] [ShutdownThread.java:51] Shutting down INFO [2017-03-15 20:39:25,712] [Main.java:135] Startup IGV Version 2.3.91 (145)02/07/2017 03:38 PM INFO [2017-03-15 20:39:25,713] [Main.java:136] Java 1.8.0_121 INFO [2017-03-15 20:39:25,713] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-15 20:39:25,720] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-15 20:39:25,720] [Main.java:138] OS: Mac OS X INFO [2017-03-15 20:39:27,354] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-15 20:39:29,592] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-15 20:39:29,680] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-15 20:40:24,363] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/AR_250_tumoronly/PCA/PCA_consensus_AR250widen_afterFDRcorrection/PCA_consensus_AR250wide_annotated_output_from_all_batches/PCA_Allmutations_SNV.vcf ERROR [2017-03-15 20:40:35,325] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-15 20:41:23,790] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/AR_250_tumoronly/highconf_250wider.bed ERROR [2017-03-15 20:41:23,872] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-15 21:11:14,842] [ShutdownThread.java:51] Shutting down INFO [2017-03-17 16:04:22,516] [Main.java:135] Startup IGV Version 2.3.91 (145)02/07/2017 03:38 PM INFO [2017-03-17 16:04:22,517] [Main.java:136] Java 1.8.0_121 INFO [2017-03-17 16:04:22,517] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-17 16:04:22,525] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-17 16:04:22,525] [Main.java:138] OS: Mac OS X INFO [2017-03-17 16:04:24,248] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-17 16:04:26,667] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-17 16:04:26,749] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-17 16:06:22,304] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/PCA_Allmutations_SNV.vcf ERROR [2017-03-17 16:06:32,209] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-17 16:06:55,302] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly ERROR [2017-03-17 16:06:55,311] [TrackLoader.java:270] /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly (Is a directory) java.io.FileNotFoundException: /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly (Is a directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138) at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:118) at org.broad.igv.util.ParsingUtils.openAsciiReader(ParsingUtils.java:90) at org.broad.igv.data.expression.ExpressionFileParser.parsableMAGE_TAB(ExpressionFileParser.java:134) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:208) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-17 16:06:55,316] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-17 16:06:55,320] [MessageUtils.java:74] /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly (Is a directory) INFO [2017-03-17 16:06:59,312] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-03-17 16:06:59,368] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-17 16:07:07,902] [ShutdownThread.java:51] Shutting down ERROR [2017-03-17 16:07:07,904] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-03-17 16:08:28,212] [Main.java:135] Startup IGV Version 2.3.91 (145)02/07/2017 03:38 PM INFO [2017-03-17 16:08:28,213] [Main.java:136] Java 1.8.0_121 INFO [2017-03-17 16:08:28,213] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-17 16:08:28,230] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-17 16:08:28,231] [Main.java:138] OS: Mac OS X INFO [2017-03-17 16:08:29,803] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-17 16:08:32,064] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-17 16:08:32,144] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-17 16:08:36,538] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/AR_250_tumoronly/PCA/PCA_consensus_AR250widen_afterFDRcorrection/PCA_consensus_AR250wide_final_output_from_all_batches/lele/PCA_union.vcf ERROR [2017-03-17 16:08:36,737] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-17 16:08:47,672] [ShutdownThread.java:51] Shutting down INFO [2017-03-17 16:39:00,867] [Main.java:135] Startup IGV Version 2.3.91 (145)02/07/2017 03:38 PM INFO [2017-03-17 16:39:00,868] [Main.java:136] Java 1.8.0_121 INFO [2017-03-17 16:39:00,868] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-17 16:39:00,874] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-17 16:39:00,874] [Main.java:138] OS: Mac OS X INFO [2017-03-17 16:39:02,370] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-17 16:39:04,793] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-17 16:39:04,893] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-17 16:39:11,236] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/lncap_high_conf_comparison/result/lncap_only.bed ERROR [2017-03-17 16:39:11,449] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-17 16:39:30,139] [ShutdownThread.java:51] Shutting down INFO [2017-03-23 14:52:26,959] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-23 14:52:26,960] [Main.java:136] Java 1.8.0_121 INFO [2017-03-23 14:52:26,960] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-23 14:52:26,967] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-23 14:52:26,967] [Main.java:138] OS: Mac OS X INFO [2017-03-23 14:52:28,770] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-23 14:52:31,100] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-23 14:52:31,184] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-23 14:52:34,228] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/AR_250_tumoronly/PCA/PCA_consensus_AR250widen_afterFDRcorrection/AR250binding_location_mutationcount/newdata/PCA_AR250_tumoronlydeneme_intersects.bed ERROR [2017-03-23 14:52:34,291] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-23 14:52:45,656] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-03-23 14:52:45,699] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-23 14:52:58,841] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-03-23 14:55:01,242] [MessageUtils.java:74] Cannot find feature or locus: >peakno_2836 INFO [2017-03-23 14:55:43,209] [ShutdownThread.java:51] Shutting down INFO [2017-03-24 16:45:10,514] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-24 16:45:10,515] [Main.java:136] Java 1.8.0_121 INFO [2017-03-24 16:45:10,515] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-24 16:45:10,521] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-24 16:45:10,522] [Main.java:138] OS: Mac OS X INFO [2017-03-24 16:45:12,165] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-24 16:45:14,916] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-24 16:45:15,020] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-24 16:46:07,186] [TrackLoader.java:126] Loading resource, path /Volumes/WINDOWSONLY/WGS/CH40.mutect_extended.KEEP.vcf INFO [2017-03-24 16:46:07,341] [TrackLoader.java:126] Loading resource, path /Volumes/WINDOWSONLY/WGS/CH41.mutect_extended.KEEP.vcf ERROR [2017-03-24 16:46:07,403] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-24 16:54:48,112] [ShutdownThread.java:51] Shutting down INFO [2017-03-24 16:54:48,139] [ShutdownThread.java:51] Shutting down INFO [2017-03-24 17:17:23,814] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-24 17:17:23,815] [Main.java:136] Java 1.8.0_121 INFO [2017-03-24 17:17:23,815] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-24 17:17:23,824] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-24 17:17:23,825] [Main.java:138] OS: Mac OS X INFO [2017-03-24 17:17:25,424] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-24 17:17:28,057] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-24 17:17:28,191] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-24 17:22:12,847] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/WGS_CHINA/Merged_All_mutect_extended.KEEP.vcf.gz ERROR [2017-03-24 17:22:13,521] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-24 17:22:46,131] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/Validation/peaksequences/AR250TumorOnlyPeakstop20_peaks.bed ERROR [2017-03-24 17:22:46,143] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-03-24 17:23:21,328] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-24 17:24:50,755] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-24 17:24:50,801] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-24 17:24:57,000] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-03-24 17:25:34,022] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-03-24 17:25:34,106] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-24 17:26:11,459] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-03-24 17:26:13,578] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-03-24 17:26:16,282] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-03-24 17:26:16,310] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-24 17:26:27,395] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/WGS_CHINA/Merged_All_mutect_extended.KEEP.vcf.gz ERROR [2017-03-24 17:26:27,531] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-24 17:26:44,215] [ShutdownThread.java:51] Shutting down ERROR [2017-03-24 17:26:44,216] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-03-24 17:31:15,632] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-24 17:31:15,632] [Main.java:136] Java 1.8.0_121 INFO [2017-03-24 17:31:15,633] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-24 17:31:15,637] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-24 17:31:15,637] [Main.java:138] OS: Mac OS X INFO [2017-03-24 17:31:17,053] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-03-24 17:31:19,411] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-03-24 17:31:19,485] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-24 17:31:25,375] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/WGS_CHINA/Merged_All_mutect_extended.KEEP.vcf.gz ERROR [2017-03-24 17:31:26,167] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-24 17:32:21,059] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-03-24 17:32:21,121] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-03-24 17:33:24,700] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-03-24 17:34:02,574] [HttpUtils.java:856] Range-byte request succeeded ERROR [2017-03-24 17:35:38,839] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-03-24 17:47:22,260] [ShutdownThread.java:51] Shutting down ERROR [2017-03-24 17:47:22,262] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-03-28 11:07:41,412] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-28 11:07:41,412] [Main.java:136] Java 1.8.0_121 INFO [2017-03-28 11:07:41,413] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-28 11:07:41,418] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-28 11:07:41,419] [Main.java:138] OS: Mac OS X INFO [2017-03-28 11:07:42,763] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-03-28 11:07:45,208] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-03-28 11:07:45,275] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-28 11:08:20,728] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/WGS_CHINA/analysis/input/Merged_All_mutect_extended.KEEP.vcf.gz ERROR [2017-03-28 11:08:21,209] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-28 11:08:33,517] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-03-28 11:08:33,596] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-28 11:09:57,256] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/PCA_AR250_tumoronlydeneme_intersects.bed ERROR [2017-03-28 11:09:57,279] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-28 11:11:13,489] [HttpUtils.java:856] Range-byte request succeeded ERROR [2017-03-28 11:11:20,157] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-03-28 11:11:20,383] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-03-28 11:12:17,267] [MessageUtils.java:74] Cannot find feature or locus: peakon_713 INFO [2017-03-28 11:12:20,632] [MessageUtils.java:74] Cannot find feature or locus: peakon_713 INFO [2017-03-28 11:15:57,306] [ShutdownThread.java:51] Shutting down ERROR [2017-03-28 11:15:57,308] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-03-30 12:04:52,653] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-30 12:04:52,654] [Main.java:136] Java 1.8.0_121 INFO [2017-03-30 12:04:52,654] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-30 12:04:52,661] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-30 12:04:52,661] [Main.java:138] OS: Mac OS X INFO [2017-03-30 12:04:54,481] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-03-30 12:04:57,590] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-03-30 12:04:57,664] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-30 12:06:16,917] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/chip-exo/GSE43785_RAW/peakcallingdeneme/deneme2_summits.bed ERROR [2017-03-30 12:06:17,042] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-30 12:06:19,384] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/chip-exo/GSE43785_RAW/peakcallingdeneme/deneme2_peaks.narrowPeak ERROR [2017-03-30 12:06:19,459] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-30 12:24:27,966] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/chip-exo/GSE43785_RAW/peakcallingdeneme/deneme2_2_peaks.narrowPeak INFO [2017-03-30 12:24:28,027] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/chip-exo/GSE43785_RAW/peakcallingdeneme/deneme2_peaks.narrowPeak ERROR [2017-03-30 12:24:28,369] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-30 12:25:51,866] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-03-30 12:34:04,097] [ShutdownThread.java:51] Shutting down INFO [2017-03-30 16:58:19,096] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-30 16:58:19,098] [Main.java:136] Java 1.8.0_121 INFO [2017-03-30 16:58:19,098] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-30 16:58:19,108] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-30 16:58:19,108] [Main.java:138] OS: Mac OS X INFO [2017-03-30 16:58:20,867] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-03-30 16:58:23,529] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-03-30 16:58:23,603] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-30 16:59:09,728] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/grch37_simplerepeats-2.bed ERROR [2017-03-30 16:59:09,766] [TrackLoader.java:270] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@31923c68, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@31923c68, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:406) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:231) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more ERROR [2017-03-30 16:59:09,772] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-30 16:59:09,777] [MessageUtils.java:74] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@31923c68, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed INFO [2017-03-30 17:00:47,588] [TrackLoader.java:126] Loading resource, path /Users/morova/lolo.bed ERROR [2017-03-30 17:00:47,624] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-30 17:16:14,996] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-30 17:16:17,221] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-30 17:16:25,693] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/grch37_simplerepeats-3.bed ERROR [2017-03-30 17:16:25,696] [TrackLoader.java:270] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@b46f9cf, for input source: /Users/morova/Downloads/grch37_simplerepeats-3.bed htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@b46f9cf, for input source: /Users/morova/Downloads/grch37_simplerepeats-3.bed at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:406) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:231) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more INFO [2017-03-30 17:16:25,696] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/grch37_simplerepeats-2.bed ERROR [2017-03-30 17:16:25,698] [TrackLoader.java:270] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@87c0021, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@87c0021, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:406) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:231) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more ERROR [2017-03-30 17:16:25,700] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-30 17:16:25,701] [MessageUtils.java:74] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@b46f9cf, for input source: /Users/morova/Downloads/grch37_simplerepeats-3.bed Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@87c0021, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed INFO [2017-03-30 17:18:23,619] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/grch37_simplerepeats-3.bed ERROR [2017-03-30 17:18:23,622] [TrackLoader.java:270] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@4b5ef256, for input source: /Users/morova/Downloads/grch37_simplerepeats-3.bed htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@4b5ef256, for input source: /Users/morova/Downloads/grch37_simplerepeats-3.bed at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:406) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:231) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more INFO [2017-03-30 17:18:23,624] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/grch37_simplerepeats-2.bed ERROR [2017-03-30 17:18:23,626] [TrackLoader.java:270] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@4af7598a, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@4af7598a, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:406) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:231) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more ERROR [2017-03-30 17:18:23,628] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-30 17:18:23,629] [MessageUtils.java:74] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@4b5ef256, for input source: /Users/morova/Downloads/grch37_simplerepeats-3.bed Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@4af7598a, for input source: /Users/morova/Downloads/grch37_simplerepeats-2.bed INFO [2017-03-30 17:18:26,589] [ShutdownThread.java:51] Shutting down ERROR [2017-03-30 17:18:26,590] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-03-30 17:18:40,982] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-30 17:18:40,983] [Main.java:136] Java 1.8.0_121 INFO [2017-03-30 17:18:40,983] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-30 17:18:41,005] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-30 17:18:41,006] [Main.java:138] OS: Mac OS X INFO [2017-03-30 17:18:43,076] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-30 17:18:45,596] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-30 17:18:45,699] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-30 19:54:57,298] [ShutdownThread.java:51] Shutting down INFO [2017-03-30 19:54:57,334] [ShutdownThread.java:51] Shutting down INFO [2017-03-31 11:00:59,518] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-31 11:00:59,519] [Main.java:136] Java 1.8.0_121 INFO [2017-03-31 11:00:59,519] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-31 11:00:59,525] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-31 11:00:59,526] [Main.java:138] OS: Mac OS X INFO [2017-03-31 11:01:01,351] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-31 11:01:03,828] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-31 11:01:03,898] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-31 11:01:08,564] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/chip-exo/GSE43785_RAW/GSM1071284_120424_ChipEXO5_NoIndex_L005_R1/GSM1071284_120424_ChipEXO5_NoIndex_L005_R1_peaks.narrowPeak ERROR [2017-03-31 11:01:08,633] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-31 11:01:23,724] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-03-31 11:02:02,868] [ShutdownThread.java:51] Shutting down INFO [2017-03-31 13:59:50,428] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-31 13:59:50,428] [Main.java:136] Java 1.8.0_121 INFO [2017-03-31 13:59:50,429] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-31 13:59:50,434] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-31 13:59:50,434] [Main.java:138] OS: Mac OS X INFO [2017-03-31 13:59:51,909] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-31 13:59:54,229] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-31 13:59:54,321] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-31 14:00:00,293] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/wgEncodeCrgMapabilityAlign100mer.Wig INFO [2017-03-31 14:00:39,687] [GenomeSummaryData.java:135] Skipping data for: chrM ERROR [2017-03-31 14:00:39,697] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-31 14:00:58,518] [ShutdownThread.java:51] Shutting down INFO [2017-03-31 16:31:16,325] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-31 16:31:16,326] [Main.java:136] Java 1.8.0_121 INFO [2017-03-31 16:31:16,326] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-31 16:31:16,333] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-31 16:31:16,333] [Main.java:138] OS: Mac OS X INFO [2017-03-31 16:31:17,771] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-31 16:31:20,348] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-31 16:31:20,426] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-31 16:31:36,153] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/Mapability/mapability_only1.Wig INFO [2017-03-31 16:31:40,333] [GenomeSummaryData.java:135] Skipping data for: chrM ERROR [2017-03-31 16:31:40,344] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-31 16:45:18,581] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/Mapability/wgEncodeCrgMapabilityAlign100mer.Wig INFO [2017-03-31 16:46:02,360] [GenomeSummaryData.java:135] Skipping data for: chrM ERROR [2017-03-31 16:46:02,365] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-31 16:46:07,479] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/AR_250_allbindinglocations/highconf_AR250allbindinglocations_hg19.bed ERROR [2017-03-31 16:46:07,603] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-31 16:46:10,500] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-03-31 16:54:51,878] [ShutdownThread.java:51] Shutting down INFO [2017-03-31 18:01:59,463] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-03-31 18:01:59,464] [Main.java:136] Java 1.8.0_121 INFO [2017-03-31 18:01:59,464] [DirectoryManager.java:72] Fetching user directory... INFO [2017-03-31 18:01:59,474] [Main.java:137] Default User Directory: /Users/morova INFO [2017-03-31 18:01:59,474] [Main.java:138] OS: Mac OS X INFO [2017-03-31 18:02:01,005] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-03-31 18:02:03,409] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-03-31 18:02:03,498] [CommandListener.java:106] Listening on port 60151 INFO [2017-03-31 18:02:08,506] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/blacklist/mysuper.bed ERROR [2017-03-31 18:02:08,638] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-31 18:02:25,997] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/blacklist/dac_duke_blacklist_unique.bed ERROR [2017-03-31 18:02:26,024] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-03-31 18:02:41,799] [ShutdownThread.java:51] Shutting down INFO [2017-04-03 09:34:50,448] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-03 09:34:50,449] [Main.java:136] Java 1.8.0_121 INFO [2017-04-03 09:34:50,449] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-03 09:34:50,455] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-03 09:34:50,456] [Main.java:138] OS: Mac OS X INFO [2017-04-03 09:34:51,826] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-03 09:34:54,268] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-03 09:34:54,346] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-03 09:35:06,930] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/Mapability/mapability_only1.Wig INFO [2017-04-03 09:35:10,926] [GenomeSummaryData.java:135] Skipping data for: chrM ERROR [2017-04-03 09:35:10,935] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-03 09:35:29,458] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/Mapability/wgEncodeCrgMapabilityAlign100mer.bigWig ERROR [2017-04-03 09:35:29,537] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-03 09:35:46,354] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-04-03 09:35:46,431] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-03 09:37:51,877] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-04-03 10:38:21,268] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/Mapability/mapability_low.bed ERROR [2017-04-03 10:38:21,370] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-03 10:52:31,795] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/Tuncs_Data/PCA_Allmutations_SNV.vcf ERROR [2017-04-03 10:52:39,365] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-03 10:53:06,426] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/Mapability/mapability100_lessthan1.Wig INFO [2017-04-03 10:53:58,655] [GenomeSummaryData.java:135] Skipping data for: chrM ERROR [2017-04-03 10:53:58,676] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-03 11:25:30,681] [ShutdownThread.java:51] Shutting down INFO [2017-04-03 16:27:54,019] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-03 16:27:54,028] [Main.java:136] Java 1.8.0_121 INFO [2017-04-03 16:27:54,028] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-03 16:27:54,042] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-03 16:27:54,043] [Main.java:138] OS: Mac OS X INFO [2017-04-03 16:27:57,076] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-03 16:28:00,126] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-03 16:28:00,234] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-03 16:28:06,186] [TrackLoader.java:126] Loading resource, path /Users/morova/LARVA/annotations/replication_timing.bw ERROR [2017-04-03 16:28:06,341] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-03 16:28:19,133] [ShutdownThread.java:51] Shutting down INFO [2017-04-05 16:31:48,512] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-05 16:31:48,513] [Main.java:136] Java 1.8.0_121 INFO [2017-04-05 16:31:48,513] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-05 16:31:48,521] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-05 16:31:48,521] [Main.java:138] OS: Mac OS X INFO [2017-04-05 16:31:50,293] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-05 16:31:52,904] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-05 16:31:52,995] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-05 16:47:11,595] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-05 16:47:11,596] [Main.java:136] Java 1.8.0_121 INFO [2017-04-05 16:47:11,596] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-05 16:47:11,601] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-05 16:47:11,602] [Main.java:138] OS: Mac OS X INFO [2017-04-05 16:47:13,166] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-05 16:47:15,867] [GenomeManager.java:192] Genome loaded. id= hg19 ERROR [2017-04-05 16:47:16,014] [CommandListener.java:124] java.net.BindException: Address already in use (Bind failed) INFO [2017-04-05 16:47:20,418] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/prosatatecancer_tf_database/Tuncs_Data/AR250_tumoronly/highconf_250wider.bed ERROR [2017-04-05 16:47:20,568] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-05 16:48:10,690] [ShutdownThread.java:51] Shutting down INFO [2017-04-06 10:53:12,756] [ShutdownThread.java:51] Shutting down INFO [2017-04-12 11:24:48,906] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-12 11:24:48,907] [Main.java:136] Java 1.8.0_121 INFO [2017-04-12 11:24:48,908] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-12 11:24:48,920] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-12 11:24:48,920] [Main.java:138] OS: Mac OS X INFO [2017-04-12 11:24:50,737] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-12 11:24:53,562] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-12 11:24:53,638] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-12 11:25:48,130] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-04-12 11:25:49,404] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-04-12 11:25:52,008] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-04-12 11:25:53,798] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-04-12 11:25:57,324] [ShutdownThread.java:51] Shutting down INFO [2017-04-18 15:15:19,906] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-18 15:15:19,907] [Main.java:136] Java 1.8.0_121 INFO [2017-04-18 15:15:19,907] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-18 15:15:19,913] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-18 15:15:19,913] [Main.java:138] OS: Mac OS X INFO [2017-04-18 15:15:21,632] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-04-18 15:15:24,614] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-04-18 15:15:24,724] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-18 15:15:29,476] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-18 15:15:31,494] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-18 15:15:33,970] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan.zip INFO [2017-04-18 15:15:36,537] [MessageUtils.java:74] Unknown file type: /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan.zip
Check file extension INFO [2017-04-18 15:15:36,906] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_abl_AR_DHT-4hr_Brown.zip INFO [2017-04-18 15:15:37,417] [MessageUtils.java:74] Unknown file type: /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_abl_AR_DHT-4hr_Brown.zip
Check file extension INFO [2017-04-18 15:15:37,953] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_VCaP_AR_No-treatment_Chinnaiyan.zip INFO [2017-04-18 15:15:38,585] [MessageUtils.java:74] Unknown file type: /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_VCaP_AR_No-treatment_Chinnaiyan.zip
Check file extension INFO [2017-04-18 15:15:39,080] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_VCaP_AR_R1881-16hr_Chinnaiyan.zip INFO [2017-04-18 15:15:39,714] [MessageUtils.java:74] Unknown file type: /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_VCaP_AR_R1881-16hr_Chinnaiyan.zip
Check file extension ERROR [2017-04-18 15:15:40,151] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 15:15:59,352] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr1.wig.gz INFO [2017-04-18 15:15:59,908] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr2.wig.gz INFO [2017-04-18 15:16:00,184] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr3.wig.gz INFO [2017-04-18 15:16:00,349] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr4.wig.gz INFO [2017-04-18 15:16:00,802] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr5.wig.gz INFO [2017-04-18 15:16:00,936] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr6.wig.gz INFO [2017-04-18 15:16:01,116] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr7.wig.gz INFO [2017-04-18 15:16:01,293] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr8.wig.gz INFO [2017-04-18 15:16:01,435] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr9.wig.gz INFO [2017-04-18 15:16:01,536] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr10.wig.gz INFO [2017-04-18 15:16:01,640] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr11.wig.gz INFO [2017-04-18 15:16:01,752] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr12.wig.gz INFO [2017-04-18 15:16:01,883] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr13.wig.gz INFO [2017-04-18 15:16:01,983] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr14.wig.gz INFO [2017-04-18 15:16:02,069] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr15.wig.gz INFO [2017-04-18 15:16:02,152] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr16.wig.gz INFO [2017-04-18 15:16:02,249] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr17.wig.gz INFO [2017-04-18 15:16:02,338] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr18.wig.gz INFO [2017-04-18 15:16:02,406] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr19.wig.gz INFO [2017-04-18 15:16:02,481] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr20.wig.gz INFO [2017-04-18 15:16:02,531] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr21.wig.gz INFO [2017-04-18 15:16:02,580] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr22.wig.gz INFO [2017-04-18 15:16:02,632] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chrX.wig.gz INFO [2017-04-18 15:16:02,710] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chrY.wig.gz ERROR [2017-04-18 15:16:02,733] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 15:19:08,116] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr13.wig INFO [2017-04-18 15:19:08,340] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr14.wig INFO [2017-04-18 15:19:08,439] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr15.wig INFO [2017-04-18 15:19:08,539] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr16.wig INFO [2017-04-18 15:19:08,683] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr17.wig INFO [2017-04-18 15:19:08,761] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr18.wig INFO [2017-04-18 15:19:08,825] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr19.wig INFO [2017-04-18 15:19:08,906] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr20.wig INFO [2017-04-18 15:19:08,975] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr21.wig INFO [2017-04-18 15:19:09,005] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chr22.wig INFO [2017-04-18 15:19:09,046] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chrX.wig INFO [2017-04-18 15:19:09,136] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/Human_22RV1_AR_No-treatment_Chinnaiyan_chrY.wig ERROR [2017-04-18 15:19:09,156] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 15:19:36,898] [ShutdownThread.java:51] Shutting down INFO [2017-04-18 15:21:26,337] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-18 15:21:26,337] [Main.java:136] Java 1.8.0_121 INFO [2017-04-18 15:21:26,338] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-18 15:21:26,349] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-18 15:21:26,349] [Main.java:138] OS: Mac OS X INFO [2017-04-18 15:21:27,764] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-18 15:21:30,567] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-18 15:21:30,730] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-18 15:21:40,429] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/wholegenome_Human_22RV1_AR_No-treatment_Chinnaiyan.wig ERROR [2017-04-18 15:21:43,979] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 15:22:14,160] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-04-18 15:22:16,216] [ShutdownThread.java:51] Shutting down INFO [2017-04-18 15:30:33,063] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-18 15:30:33,063] [Main.java:136] Java 1.8.0_121 INFO [2017-04-18 15:30:33,063] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-18 15:30:33,071] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-18 15:30:33,071] [Main.java:138] OS: Mac OS X INFO [2017-04-18 15:30:34,784] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-18 15:30:37,498] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-18 15:30:37,579] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-18 15:31:05,032] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/wholegenome_Human_22RV1_AR_No-treatment_Chinnaiyan.wig INFO [2017-04-18 15:31:08,344] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_abl_AR_DHT-4hr_Brown/wholegenome_Human_abl_AR_DHT-4hr_Brown.wig INFO [2017-04-18 15:31:59,104] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_VCaP_AR_No-treatment_Chinnaiyan/wholegenome_Human_VCaP_AR_No-treatment_Chinnaiyan.wig INFO [2017-04-18 15:32:06,559] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_VCaP_AR_R1881-16hr_Chinnaiyan/wholegenome_Human_VCaP_AR_R1881-16hr_Chinnaiyan.wig ERROR [2017-04-18 15:32:20,628] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 15:35:54,650] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_VCaP_AR_R1881-16hr_Chinnaiyan/wholegenome_Human_VCaP_AR_R1881-16hr_Chinnaiyan.wig ERROR [2017-04-18 15:36:29,405] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 15:58:13,489] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_abl_AR_DHT-4hr_Brown 2/Human_abl_AR_DHT-4hr_Brown_chr1.wig.gz ERROR [2017-04-18 15:58:21,738] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 15:58:47,570] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-04-18 16:17:49,794] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_22RV1_AR_No-treatment_Chinnaiyan/wholegenome_Human_22RV1_AR_No-treatment_Chinnaiyan.wig ERROR [2017-04-18 16:17:58,705] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 16:18:58,952] [TrackLoader.java:126] Loading resource, path /Volumes/Data/Lack Lab sequencing/Prostate AR ChipSeq/Human_abl_AR_DHT-4hr_Brown/wholegenome_Human_abl_AR_DHT-4hr_Brown.wig ERROR [2017-04-18 16:19:56,442] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-18 16:19:56,688] [ShutdownThread.java:51] Shutting down INFO [2017-04-20 13:53:19,117] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-20 13:53:19,118] [Main.java:136] Java 1.8.0_131 INFO [2017-04-20 13:53:19,118] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-20 13:53:19,127] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-20 13:53:19,127] [Main.java:138] OS: Mac OS X INFO [2017-04-20 13:53:20,826] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-20 13:53:23,398] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-20 13:53:23,491] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-20 13:53:27,516] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TaskER/MCF7/ENCFF040STP.bed.gz INFO [2017-04-20 13:53:27,755] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TaskER/MCF7/ENCFF953SEZ.bed.gz ERROR [2017-04-20 13:53:27,975] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-20 14:48:53,563] [ShutdownThread.java:51] Shutting down INFO [2017-04-21 09:23:59,910] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-21 09:23:59,911] [Main.java:136] Java 1.8.0_131 INFO [2017-04-21 09:23:59,912] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-21 09:23:59,924] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-21 09:23:59,925] [Main.java:138] OS: Mac OS X INFO [2017-04-21 09:24:03,058] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-21 09:24:07,487] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-21 09:24:07,588] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-21 09:33:07,711] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-21 09:33:10,661] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-21 09:33:11,574] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/lncap_abl_ar/GSM969565_abl-VEH-AR-hs-sd_treat_pileup.bw ERROR [2017-04-21 09:33:11,795] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-21 09:33:17,345] [ShutdownThread.java:51] Shutting down INFO [2017-04-21 10:22:44,692] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-21 10:22:44,694] [Main.java:136] Java 1.8.0_131 INFO [2017-04-21 10:22:44,694] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-21 10:22:44,701] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-21 10:22:44,701] [Main.java:138] OS: Mac OS X INFO [2017-04-21 10:22:46,623] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-21 10:22:49,664] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-21 10:22:49,747] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-21 10:23:09,548] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bedGraph_hg19 INFO [2017-04-21 10:23:12,553] [MessageUtils.java:74] Unknown file type: /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bedGraph_hg19
Check file extension INFO [2017-04-21 10:23:13,932] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw ERROR [2017-04-21 10:23:14,059] [BBFileReader.java:137] BBFile header is unrecognized type, header magic = 0 ERROR [2017-04-21 10:23:14,061] [TrackLoader.java:270] Error reading BBFile header for: /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw java.lang.RuntimeException: Error reading BBFile header for: /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw at org.broad.igv.bbfile.BBFileReader.(BBFileReader.java:138) at org.broad.igv.track.TrackLoader.loadBWFile(TrackLoader.java:776) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:195) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-04-21 10:23:14,072] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-21 10:23:14,073] [MessageUtils.java:74] Error reading BBFile header for: /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw INFO [2017-04-21 10:23:18,621] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw ERROR [2017-04-21 10:23:18,629] [BBFileReader.java:137] BBFile header is unrecognized type, header magic = 0 ERROR [2017-04-21 10:23:18,630] [TrackLoader.java:270] Error reading BBFile header for: /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw java.lang.RuntimeException: Error reading BBFile header for: /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw at org.broad.igv.bbfile.BBFileReader.(BBFileReader.java:138) at org.broad.igv.track.TrackLoader.loadBWFile(TrackLoader.java:776) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:195) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-04-21 10:23:18,632] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-21 10:23:18,634] [MessageUtils.java:74] Error reading BBFile header for: /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984389_CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bw INFO [2017-04-21 12:23:19,301] [ShutdownThread.java:51] Shutting down ERROR [2017-04-21 12:23:19,312] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-04-21 15:04:54,861] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-21 15:04:54,862] [Main.java:136] Java 1.8.0_131 INFO [2017-04-21 15:04:54,862] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-21 15:04:54,876] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-21 15:04:54,876] [Main.java:138] OS: Mac OS X INFO [2017-04-21 15:04:56,752] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-21 15:04:59,332] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-21 15:04:59,399] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-21 15:05:03,275] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/22RV1_ar/GSM984390_CHIPSEQ.22RV1_AR_TREATED.337.s_1_306.s_5_442.1.s_5.ATCT.bedGraph INFO [2017-04-21 15:07:20,153] [ShutdownThread.java:51] Shutting down INFO [2017-04-21 15:08:49,565] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-21 15:08:49,565] [Main.java:136] Java 1.8.0_131 INFO [2017-04-21 15:08:49,566] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-21 15:08:49,576] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-21 15:08:49,576] [Main.java:138] OS: Mac OS X INFO [2017-04-21 15:08:51,672] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-21 15:08:54,854] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-21 15:08:54,923] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-21 15:08:59,030] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/lncap_abl_ar/GSM969565_abl-VEH-AR-hs-sd_treat_pileup.bigWig ERROR [2017-04-21 15:08:59,748] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-21 15:09:28,272] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-21 15:09:30,099] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-21 15:09:33,710] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/vcap/GSM1328947_VcaP_AR_VEH_DHTn_yes_2.bw INFO [2017-04-21 15:09:34,320] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/vcap/GSM1328947_VcaP_AR_VEH_DHTn_yes_2.bw.1 INFO [2017-04-21 15:09:36,634] [MessageUtils.java:74] Unknown file type: /Volumes/blackhole/NathanTracks/vcap/GSM1328947_VcaP_AR_VEH_DHTn_yes_2.bw.1
Check file extension ERROR [2017-04-21 15:09:38,081] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-21 15:14:10,096] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/vcap/GSM1328947_VcaP_AR_VEH_DHTn_yes_2.bw INFO [2017-04-21 15:14:10,578] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/vcap/GSM1328952_VcaP_AR_VEH_DHTp_yes_2.bw ERROR [2017-04-21 15:14:10,624] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-21 15:14:48,922] [ShutdownThread.java:51] Shutting down INFO [2017-04-21 16:09:13,087] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-21 16:09:13,088] [Main.java:136] Java 1.8.0_131 INFO [2017-04-21 16:09:13,088] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-21 16:09:13,100] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-21 16:09:13,104] [Main.java:138] OS: Mac OS X INFO [2017-04-21 16:09:15,308] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-21 16:09:18,368] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-21 16:09:18,515] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-21 16:09:26,591] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-21 16:09:28,626] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-21 16:09:33,600] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/C42B/GSM984381_CHIPSEQ.C42B_AR_VEHICLE_2.692.s_1_710.s_6.CGTCGCT.bw INFO [2017-04-21 16:09:34,213] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/NathanTracks/C42B/GSM984383_CHIPSEQ.C42B_AR_TREATED_1.465.s_4.AGTT.bw ERROR [2017-04-21 16:09:34,390] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-21 16:31:15,452] [ShutdownThread.java:51] Shutting down INFO [2017-04-21 16:31:15,472] [ShutdownThread.java:51] Shutting down INFO [2017-04-24 14:53:48,704] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-24 14:53:48,704] [Main.java:136] Java 1.8.0_131 INFO [2017-04-24 14:53:48,705] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-24 14:53:48,711] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-24 14:53:48,711] [Main.java:138] OS: Mac OS X INFO [2017-04-24 14:53:50,361] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-24 14:53:52,610] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-24 14:53:52,683] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-24 14:53:57,267] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/Estrogen_Receptor_Runs/Beds/T47D/encode/ESR1/T47D_ER_10k.bed ERROR [2017-04-24 14:53:57,439] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-24 14:54:42,961] [ShutdownThread.java:51] Shutting down INFO [2017-04-25 11:20:38,162] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-25 11:20:38,163] [Main.java:136] Java 1.8.0_131 INFO [2017-04-25 11:20:38,163] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-25 11:20:38,181] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-25 11:20:38,182] [Main.java:138] OS: Mac OS X INFO [2017-04-25 11:20:39,813] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-25 11:20:42,249] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-25 11:20:42,311] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-25 11:20:43,402] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/gap_regions_grch37.bed ERROR [2017-04-25 11:20:43,450] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-25 11:20:51,637] [ShutdownThread.java:51] Shutting down INFO [2017-04-25 13:58:21,651] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-25 13:58:21,652] [Main.java:136] Java 1.8.0_131 INFO [2017-04-25 13:58:21,652] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-25 13:58:21,659] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-25 13:58:21,660] [Main.java:138] OS: Mac OS X INFO [2017-04-25 13:58:23,457] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-25 13:58:26,170] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-25 13:58:26,255] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-25 15:22:48,805] [ShutdownThread.java:51] Shutting down INFO [2017-04-26 15:08:13,150] [Main.java:135] Startup IGV Version 2.3.92 (146)03/22/2017 08:15 PM INFO [2017-04-26 15:08:13,150] [Main.java:136] Java 1.8.0_131 INFO [2017-04-26 15:08:13,151] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-26 15:08:13,164] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-26 15:08:13,164] [Main.java:138] OS: Mac OS X INFO [2017-04-26 15:08:14,850] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-26 15:08:17,552] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-26 15:08:17,699] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-26 15:08:21,674] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/LNCAP_Marks/LNCAP_RNAseq/lncap_dht2/lncap_dht2.bam ERROR [2017-04-26 15:08:21,748] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-26 15:08:34,547] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-04-26 15:09:06,373] [ShutdownThread.java:51] Shutting down INFO [2017-04-28 12:38:11,388] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-04-28 12:38:11,389] [Main.java:136] Java 1.8.0_131 INFO [2017-04-28 12:38:11,389] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-28 12:38:11,396] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-28 12:38:11,396] [Main.java:138] OS: Mac OS X INFO [2017-04-28 12:38:13,571] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-04-28 12:38:15,797] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-04-28 12:38:15,870] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-28 12:38:36,333] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-04-28 12:38:37,510] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-04-28 12:38:50,187] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-28 12:38:52,057] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-28 14:02:36,446] [ShutdownThread.java:51] Shutting down INFO [2017-04-28 15:58:05,724] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-04-28 15:58:05,725] [Main.java:136] Java 1.8.0_131 INFO [2017-04-28 15:58:05,725] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-28 15:58:05,731] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-28 15:58:05,731] [Main.java:138] OS: Mac OS X INFO [2017-04-28 15:58:07,219] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-04-28 15:58:09,614] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-04-28 15:58:09,698] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-28 15:58:38,957] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/random_thing/polyA_beds/randombeds/sorted_randomization_1k.bed ERROR [2017-04-28 15:58:41,251] [TrackLoader.java:270] An index is required, but none found., for input source: /Volumes/blackhole/random_thing/polyA_beds/randombeds/sorted_randomization_1k.bed htsjdk.tribble.TribbleException: An index is required, but none found., for input source: /Volumes/blackhole/random_thing/polyA_beds/randombeds/sorted_randomization_1k.bed at htsjdk.tribble.TribbleIndexedFeatureReader.(TribbleIndexedFeatureReader.java:111) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:89) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:91) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:406) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:231) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-04-28 15:58:41,256] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-28 15:58:41,258] [MessageUtils.java:74] An index is required, but none found., for input source: /Volumes/blackhole/random_thing/polyA_beds/randombeds/sorted_randomization_1k.bed INFO [2017-04-28 15:59:46,165] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-04-28 15:59:48,310] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-04-28 16:03:21,499] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/random_thing/polyA_beds/randombeds/sorted_randomization_1k.bed.gz INFO [2017-04-28 16:04:56,826] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-04-28 16:04:56,826] [Main.java:136] Java 1.8.0_131 INFO [2017-04-28 16:04:56,827] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-28 16:04:56,836] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-28 16:04:56,837] [Main.java:138] OS: Mac OS X INFO [2017-04-28 16:04:59,071] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/1kg_v37.genome INFO [2017-04-28 16:05:02,030] [GenomeManager.java:192] Genome loaded. id= 1kg_v37 INFO [2017-04-28 16:05:02,156] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-28 16:05:09,481] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/random_thing/polyA_beds/randombeds/sorted_randomization_1k.bed INFO [2017-04-28 16:06:06,629] [MessageUtils.java:74] ERROR [2017-04-28 16:06:06,632] [TrackLoader.java:270] java.lang.NullPointerException at org.broad.igv.ui.util.MessageUtils.showMessage(MessageUtils.java:78) at org.broad.igv.ui.util.MessageUtils.showMessage(MessageUtils.java:69) at org.broad.igv.ui.util.IndexCreatorDialog.getIndex(IndexCreatorDialog.java:132) at org.broad.igv.track.TribbleFeatureSource.createIndex(TribbleFeatureSource.java:117) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:85) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:406) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:231) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-04-28 16:06:06,637] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-28 16:07:18,719] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-04-28 16:07:20,594] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-04-28 16:16:23,973] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/random_thing/polyA_beds/randombeds/sorted_randomization_1k.bed.gz ERROR [2017-04-28 16:16:24,465] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-28 16:19:26,715] [ShutdownThread.java:51] Shutting down ERROR [2017-04-28 16:19:26,723] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NoClassDefFoundError: org/broad/igv/dev/db/DBManager at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) Caused by: java.lang.ClassNotFoundException: org.broad.igv.dev.db.DBManager at java.net.URLClassLoader$1.run(URLClassLoader.java:370) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 2 more Caused by: java.io.IOException: Stream closed at java.util.zip.InflaterInputStream.ensureOpen(InflaterInputStream.java:67) at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:142) at sun.misc.Resource.getBytes(Resource.java:124) at java.net.URLClassLoader.defineClass(URLClassLoader.java:462) at java.net.URLClassLoader.access$100(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:368) ... 9 more INFO [2017-04-28 16:59:45,043] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-04-28 16:59:45,044] [Main.java:136] Java 1.8.0_131 INFO [2017-04-28 16:59:45,044] [DirectoryManager.java:72] Fetching user directory... INFO [2017-04-28 16:59:45,057] [Main.java:137] Default User Directory: /Users/morova INFO [2017-04-28 16:59:45,058] [Main.java:138] OS: Mac OS X INFO [2017-04-28 16:59:46,686] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-04-28 16:59:48,340] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-04-28 16:59:48,415] [CommandListener.java:106] Listening on port 60151 INFO [2017-04-28 16:59:57,785] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/random_thing/polyA_beds/randombeds/randomization_1k.bw ERROR [2017-04-28 16:59:58,113] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-28 17:04:53,983] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/gap_regions_grch37.bed ERROR [2017-04-28 17:04:54,033] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-04-28 17:06:38,301] [ShutdownThread.java:51] Shutting down INFO [2017-05-04 14:25:42,003] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-05-04 14:25:42,004] [Main.java:136] Java 1.8.0_131 INFO [2017-05-04 14:25:42,005] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-04 14:25:42,015] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-04 14:25:42,016] [Main.java:138] OS: Mac OS X INFO [2017-05-04 14:25:44,491] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-05-04 14:25:46,978] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-05-04 14:25:47,208] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-04 14:27:29,033] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF001TON.bed.gz INFO [2017-05-04 14:27:40,973] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF001TOO.bed.gz ERROR [2017-05-04 14:28:05,282] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-04 14:28:11,802] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-04 14:28:14,677] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-04 14:29:13,532] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF001TON.bed.gz INFO [2017-05-04 14:29:23,334] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF001TOO.bed.gz ERROR [2017-05-04 14:29:36,336] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-04 14:39:03,845] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-04 14:42:38,677] [ShutdownThread.java:51] Shutting down INFO [2017-05-05 10:37:20,731] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-05-05 10:37:20,733] [Main.java:136] Java 1.8.0_131 INFO [2017-05-05 10:37:20,734] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-05 10:37:20,742] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-05 10:37:20,743] [Main.java:138] OS: Mac OS X INFO [2017-05-05 10:37:22,659] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-05 10:37:25,400] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-05 10:37:25,483] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-05 10:37:31,124] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-05 10:37:33,414] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-05 10:37:40,167] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/LNCAP_Marks/HistoneMarks/LNCAP_H3K9me3/GSM353610_20FALAAXX_C256.allregions.bed ERROR [2017-05-05 10:37:40,337] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-05 10:38:09,024] [MessageUtils.java:74] Cannot find feature or locus: 57435651 INFO [2017-05-05 10:38:16,763] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-05 11:19:26,425] [ShutdownThread.java:51] Shutting down INFO [2017-05-07 17:59:03,126] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-05-07 17:59:03,127] [Main.java:136] Java 1.8.0_131 INFO [2017-05-07 17:59:03,127] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-07 17:59:03,133] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-07 17:59:03,134] [Main.java:138] OS: Mac OS X INFO [2017-05-07 17:59:04,853] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-07 17:59:07,903] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-07 17:59:08,005] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-07 17:59:32,571] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ENCFF001TOO.bed ERROR [2017-05-07 17:59:45,377] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-07 18:59:24,648] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-07 19:02:25,071] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/ENCFF001TON.bed ERROR [2017-05-07 19:02:36,745] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-08 09:51:58,406] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/LNCAP_CpG_ENCFF001TOO.bed ERROR [2017-05-08 09:52:12,348] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-08 10:23:09,655] [ShutdownThread.java:51] Shutting down INFO [2017-05-08 10:29:02,223] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-05-08 10:29:02,224] [Main.java:136] Java 1.8.0_131 INFO [2017-05-08 10:29:02,224] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-08 10:29:02,232] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-08 10:29:02,232] [Main.java:138] OS: Mac OS X INFO [2017-05-08 10:29:04,031] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-08 10:29:07,015] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-08 10:29:07,126] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-08 10:29:32,860] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/LNCAP_CpG_ENCFF001TOO.bed ERROR [2017-05-08 10:29:37,618] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-08 10:30:03,024] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-08 13:20:13,308] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-08 13:20:16,808] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-08 14:57:32,542] [ShutdownThread.java:51] Shutting down INFO [2017-05-09 17:29:16,559] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-05-09 17:29:16,561] [Main.java:136] Java 1.8.0_131 INFO [2017-05-09 17:29:16,562] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-09 17:29:16,575] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-09 17:29:16,575] [Main.java:138] OS: Mac OS X INFO [2017-05-09 17:29:18,081] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-09 17:29:20,491] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-09 17:29:20,569] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-09 17:29:27,785] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/46wayConservation/chr1.phastCons46way.bw ERROR [2017-05-09 17:29:27,916] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-10 10:56:32,347] [ShutdownThread.java:51] Shutting down INFO [2017-05-10 10:56:32,400] [ShutdownThread.java:51] Shutting down INFO [2017-05-11 19:06:01,794] [Main.java:135] Startup IGV Version 2.3.92 (147)04/27/2017 10:54 PM INFO [2017-05-11 19:06:01,794] [Main.java:136] Java 1.8.0_131 INFO [2017-05-11 19:06:01,795] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-11 19:06:01,800] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-11 19:06:01,801] [Main.java:138] OS: Mac OS X INFO [2017-05-11 19:06:03,812] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-11 19:06:06,458] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-11 19:06:06,533] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-11 19:06:10,850] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/LNCAP_Marks/TF/GSM2122802_GRHL2_1.bigwig ERROR [2017-05-11 19:06:11,508] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-11 19:06:13,983] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/LNCAP_Marks/TF/GRHL2.bed ERROR [2017-05-11 19:06:14,108] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-11 19:06:33,666] [ShutdownThread.java:51] Shutting down INFO [2017-05-15 09:46:42,086] [Main.java:135] Startup IGV Version 2.3.93 (149)05/13/2017 08:29 PM INFO [2017-05-15 09:46:42,087] [Main.java:136] Java 1.8.0_131 INFO [2017-05-15 09:46:42,087] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-15 09:46:42,096] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-15 09:46:42,097] [Main.java:138] OS: Mac OS X INFO [2017-05-15 09:46:43,741] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-15 09:46:46,431] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-15 09:46:46,628] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-15 09:50:36,126] [TrackLoader.java:126] Loading resource, path /Users/morova/35553150-e4ef-4539-b220-259f2d634bd7.svcp_1-0-7.20150621.somatic.snv_mnv.vcf.gz ERROR [2017-05-15 09:50:39,301] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-05-15 09:50:57,448] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.ui.action.SearchCommand.askUserFeature(SearchCommand.java:317) at org.broad.igv.ui.action.SearchCommand.execute(SearchCommand.java:136) at org.broad.igv.ui.IGVCommandBar.searchByLocus(IGVCommandBar.java:960) at org.broad.igv.ui.IGVCommandBar.goButtonActionPerformed(IGVCommandBar.java:944) at org.broad.igv.ui.IGVCommandBar.access$200(IGVCommandBar.java:83) at org.broad.igv.ui.IGVCommandBar$3.actionPerformed(IGVCommandBar.java:205) at javax.swing.JTextField.fireActionPerformed(JTextField.java:508) at javax.swing.JTextField.postActionEvent(JTextField.java:721) at javax.swing.JTextField$NotifyAction.actionPerformed(JTextField.java:836) at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1663) at javax.swing.JComponent.processKeyBinding(JComponent.java:2882) at javax.swing.JComponent.processKeyBindings(JComponent.java:2929) at javax.swing.JComponent.processKeyEvent(JComponent.java:2845) at java.awt.Component.processEvent(Component.java:6310) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954) at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(DefaultKeyboardFocusManager.java:806) at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(DefaultKeyboardFocusManager.java:1074) at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:945) at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:771) at java.awt.Component.dispatchEventImpl(Component.java:4760) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-05-15 09:52:55,456] [TrackLoader.java:126] Loading resource, path /Users/morova/35553150-e4ef-4539-b220-259f2d634bd7.svcp_1-0-7.20150621.somatic.cnv.vcf.gz ERROR [2017-05-15 09:52:55,509] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-05-15 09:56:48,093] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-05-15 09:56:48,400] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-05-15 10:06:34,754] [ShutdownThread.java:51] Shutting down ERROR [2017-05-15 10:06:34,760] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-05-15 11:05:03,630] [Main.java:135] Startup IGV Version 2.3.93 (149)05/13/2017 08:29 PM INFO [2017-05-15 11:05:03,631] [Main.java:136] Java 1.8.0_131 INFO [2017-05-15 11:05:03,632] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-15 11:05:03,647] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-15 11:05:03,647] [Main.java:138] OS: Mac OS X INFO [2017-05-15 11:05:05,602] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-15 11:05:08,336] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-15 11:05:08,428] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-15 11:10:17,271] [TrackLoader.java:126] Loading resource, path /Users/morova/98f54445-b151-4aeb-b8cf-91d743ba066e.embl-delly_1-0-0-preFilter.20150814.somatic.sv.vcf.gz ERROR [2017-05-15 11:10:17,434] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-15 12:29:22,931] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/broad_data/input/1d63d338-cdee-4caf-8684-768243574938/005e85a3-3571-462d-8dc9-2babfc7ace21.broad-dRanger_snowman.20151023.somatic.sv.vcf.gz ERROR [2017-05-15 12:29:22,994] [TrackLoader.java:275] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 java.lang.RuntimeException: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189) at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:138) at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:200) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:93) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:156) at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:181) ... 43 more ERROR [2017-05-15 12:29:22,999] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-15 12:29:23,002] [MessageUtils.java:74] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 INFO [2017-05-15 12:30:03,785] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/broad_data/input/1d63d338-cdee-4caf-8684-768243574938/005e85a3-3571-462d-8dc9-2babfc7ace21.broad-dRanger.20151023.somatic.sv.vcf.gz.idx ERROR [2017-05-15 12:30:03,802] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-15 18:34:06,034] [ShutdownThread.java:51] Shutting down INFO [2017-05-15 18:34:06,369] [ShutdownThread.java:51] Shutting down INFO [2017-05-16 16:17:37,552] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-16 16:17:37,553] [Main.java:136] Java 1.8.0_131 INFO [2017-05-16 16:17:37,553] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-16 16:17:37,560] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-16 16:17:37,560] [Main.java:138] OS: Mac OS X INFO [2017-05-16 16:17:39,211] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-16 16:17:41,772] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-16 16:17:41,849] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-16 16:17:46,332] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/annotated.32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf ERROR [2017-05-16 16:17:48,293] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 55: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/annotated.32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 55: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/annotated.32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-05-16 16:17:48,304] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-16 16:17:48,305] [MessageUtils.java:74] The provided VCF file is malformed at approximately line number 55: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/annotated.32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf INFO [2017-05-16 16:17:54,440] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf ERROR [2017-05-16 16:17:54,455] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 50: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 50: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-05-16 16:17:54,458] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-16 16:17:54,458] [MessageUtils.java:74] The provided VCF file is malformed at approximately line number 50: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf INFO [2017-05-16 16:17:59,672] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv copy.vcf ERROR [2017-05-16 16:17:59,783] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-16 16:18:21,541] [ShutdownThread.java:51] Shutting down ERROR [2017-05-16 16:18:21,542] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-05-17 11:01:11,743] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-17 11:01:11,744] [Main.java:136] Java 1.8.0_131 INFO [2017-05-17 11:01:11,744] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-17 11:01:11,750] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-17 11:01:11,751] [Main.java:138] OS: Mac OS X INFO [2017-05-17 11:01:13,512] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-17 11:01:16,347] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-17 11:01:16,425] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-17 11:01:19,798] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf ERROR [2017-05-17 11:01:19,892] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 50: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 50: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-05-17 11:01:19,898] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:01:19,904] [MessageUtils.java:74] The provided VCF file is malformed at approximately line number 50: unparsable vcf record with allele BND, for input source: /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf INFO [2017-05-17 11:01:24,350] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv copy.vcf ERROR [2017-05-17 11:01:24,470] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:01:33,782] [MessageUtils.java:74] Cannot find feature or locus: BRCA ERROR [2017-05-17 11:01:49,693] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-05-17 11:01:49,971] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-05-17 11:02:21,603] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-17 11:14:37,926] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/sv/2be414dc-cea3-11e5-a663-d6714d100685/2ea2294d-fab9-43ae-a222-370487495b06.svfix2_4-0-12.20160208.somatic.sv.vcf.gz ERROR [2017-05-17 11:14:37,977] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:16:40,506] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/sv/2be414dc-cea3-11e5-a663-d6714d100685/seqware-results/0/caveman/2ea2294d-fab9-43ae-a222-370487495b06_vs_8bd619f6-0f73-4cbf-ae94-36217bf66fe6.flagged.muts.vcf.gz ERROR [2017-05-17 11:16:40,553] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:22:49,494] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-snowman.20151215.somatic.sv.vcf.gz ERROR [2017-05-17 11:22:49,513] [TrackLoader.java:275] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 java.lang.RuntimeException: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189) at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:138) at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:200) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:93) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:156) at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:181) ... 43 more ERROR [2017-05-17 11:22:49,515] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:22:49,515] [MessageUtils.java:74] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 INFO [2017-05-17 11:23:01,182] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-dRanger.20151215.somatic.sv.vcf.gz ERROR [2017-05-17 11:23:01,194] [TrackLoader.java:275] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 java.lang.RuntimeException: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189) at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:138) at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:200) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:93) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:156) at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:181) ... 43 more ERROR [2017-05-17 11:23:01,195] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:23:01,196] [MessageUtils.java:74] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 INFO [2017-05-17 11:23:10,720] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-dRanger.20151215.somatic.sv.vcf ERROR [2017-05-17 11:23:10,740] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:23:36,799] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-snowman.20151215.somatic.sv.vcf ERROR [2017-05-17 11:23:36,822] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:24:11,105] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-snowman.20151215.somatic.indel.vcf.gz ERROR [2017-05-17 11:24:11,116] [TrackLoader.java:275] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 java.lang.RuntimeException: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189) at htsjdk.tribble.TribbleIndexedFeatureReader.loadIndex(TribbleIndexedFeatureReader.java:138) at htsjdk.tribble.TribbleIndexedFeatureReader.hasIndex(TribbleIndexedFeatureReader.java:200) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:93) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 at htsjdk.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:156) at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:181) ... 43 more ERROR [2017-05-17 11:24:11,117] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:24:11,118] [MessageUtils.java:74] htsjdk.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type. magic number: 0x4088b1f; type 0 INFO [2017-05-17 11:24:15,385] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-snowman.20151215.somatic.indel.vcf ERROR [2017-05-17 11:24:15,387] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 30: there are 1 genotypes while the header requires that 2 genotypes be present for all records at 1:4363058, for input source: /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-snowman.20151215.somatic.indel.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 30: there are 1 genotypes while the header requires that 2 genotypes be present for all records at 1:4363058, for input source: /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-snowman.20151215.somatic.indel.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:662) at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:128) at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158) at htsjdk.variant.variantcontext.LazyGenotypesContext.ensureSampleNameMap(LazyGenotypesContext.java:180) at htsjdk.variant.variantcontext.GenotypesContext.getSampleNames(GenotypesContext.java:646) at htsjdk.variant.variantcontext.VariantContext.getSampleNames(VariantContext.java:994) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:72) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-05-17 11:24:15,389] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:24:15,389] [MessageUtils.java:74] The provided VCF file is malformed at approximately line number 30: there are 1 genotypes while the header requires that 2 genotypes be present for all records at 1:4363058, for input source: /Users/morova/SV_data/broad/08ec408c-1a92-4136-9be2-461a480068fc/f9c0a08b-d1e5-4c18-e040-11ac0c4864df.broad-snowman.20151215.somatic.indel.vcf INFO [2017-05-17 11:32:20,540] [ShutdownThread.java:51] Shutting down ERROR [2017-05-17 11:32:20,544] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-05-17 11:40:46,449] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-17 11:40:46,450] [Main.java:136] Java 1.8.0_131 INFO [2017-05-17 11:40:46,451] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-17 11:40:46,470] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-17 11:40:46,470] [Main.java:138] OS: Mac OS X INFO [2017-05-17 11:40:47,939] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-17 11:40:50,437] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-17 11:40:50,523] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-17 11:40:53,316] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/interested_gene_list.bed ERROR [2017-05-17 11:40:53,376] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:41:41,103] [ShutdownThread.java:51] Shutting down INFO [2017-05-17 11:41:41,114] [ShutdownThread.java:51] Shutting down INFO [2017-05-17 11:47:30,495] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-17 11:47:30,496] [Main.java:136] Java 1.8.0_131 INFO [2017-05-17 11:47:30,497] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-17 11:47:30,501] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-17 11:47:30,502] [Main.java:138] OS: Mac OS X INFO [2017-05-17 11:47:32,382] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-17 11:47:35,292] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-17 11:47:35,397] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-17 11:47:42,050] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/fa49cdc9-03f2-47c7-9e78-de631400915c/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.bedpe ERROR [2017-05-17 11:47:42,136] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:47:49,675] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/fa49cdc9-03f2-47c7-9e78-de631400915c/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.bedpe.txt ERROR [2017-05-17 11:47:49,759] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:48:15,058] [ShutdownThread.java:51] Shutting down INFO [2017-05-17 11:55:38,714] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-17 11:55:38,717] [Main.java:136] Java 1.8.0_131 INFO [2017-05-17 11:55:38,718] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-17 11:55:38,733] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-17 11:55:38,733] [Main.java:138] OS: Mac OS X INFO [2017-05-17 11:55:40,610] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-17 11:55:43,014] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-17 11:55:43,146] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-17 11:55:45,477] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/fa49cdc9-03f2-47c7-9e78-de631400915c/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf ERROR [2017-05-17 11:55:45,637] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 11:59:24,459] [MessageUtils.java:74] Cannot find feature or locus: chr20PTEN INFO [2017-05-17 12:06:29,995] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/fa49cdc9-03f2-47c7-9e78-de631400915c/32d8c373-b5c8-420b-9808-8812b5501649.dkfz-indelCalling_1-0-132-1.20150820.somatic.indel.vcf.gz ERROR [2017-05-17 12:06:30,113] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 12:07:00,484] [ShutdownThread.java:51] Shutting down INFO [2017-05-17 12:08:08,273] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-17 12:08:08,273] [Main.java:136] Java 1.8.0_131 INFO [2017-05-17 12:08:08,273] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-17 12:08:08,277] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-17 12:08:08,277] [Main.java:138] OS: Mac OS X INFO [2017-05-17 12:08:09,665] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-17 12:08:12,211] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-17 12:08:12,284] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-17 12:08:14,507] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/embl/results.vcf ERROR [2017-05-17 12:08:14,539] [TrackLoader.java:275] Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /Users/morova/SV_data/embl/results.vcf htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /Users/morova/SV_data/embl/results.vcf at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:231) at htsjdk.tribble.TribbleIndexedFeatureReader.(TribbleIndexedFeatureReader.java:92) at htsjdk.tribble.TribbleIndexedFeatureReader.(TribbleIndexedFeatureReader.java:103) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:89) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:91) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:115) at org.broad.igv.feature.tribble.VCFWrapperCodec.readActualHeader(VCFWrapperCodec.java:92) at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:88) at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:229) ... 44 more ERROR [2017-05-17 12:08:14,544] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 12:08:14,546] [MessageUtils.java:74] Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /Users/morova/SV_data/embl/results.vcf INFO [2017-05-17 12:08:31,295] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/embl/results.vcf ERROR [2017-05-17 12:08:31,333] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 12:08:38,382] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/interested_gene_list.bed ERROR [2017-05-17 12:08:38,392] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 12:14:10,085] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/fa49cdc9-03f2-47c7-9e78-de631400915c/32d8c373-b5c8-420b-9808-8812b5501649.dkfz-copyNumberEstimation_1-0-189.20150820.somatic.cnv.vcf ERROR [2017-05-17 12:14:10,700] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-05-17 12:25:14,916] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-05-17 12:26:24,038] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-17 12:29:49,878] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/fa49cdc9-03f2-47c7-9e78-de631400915c/32d8c373-b5c8-420b-9808-8812b5501649.dkfz-copyNumberEstimation_1-0-189.20150820.somatic.cnv.vcf.gz ERROR [2017-05-17 12:29:49,933] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-05-17 12:32:14,062] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-05-17 12:44:15,727] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/embl/cnv_result.vcf ERROR [2017-05-17 12:44:15,758] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 12:45:32,354] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/interested_gene_list.bed ERROR [2017-05-17 12:45:32,358] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 13:16:18,355] [ShutdownThread.java:51] Shutting down INFO [2017-05-17 13:16:18,383] [ShutdownThread.java:51] Shutting down INFO [2017-05-17 14:53:34,832] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-17 14:53:34,833] [Main.java:136] Java 1.8.0_131 INFO [2017-05-17 14:53:34,834] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-17 14:53:34,851] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-17 14:53:34,851] [Main.java:138] OS: Mac OS X INFO [2017-05-17 14:53:36,375] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-17 14:53:38,764] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-17 14:53:38,871] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-17 14:53:42,689] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/embl/result_SV.vcf ERROR [2017-05-17 14:53:42,774] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 14:54:11,740] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/interested_gene_list.bed ERROR [2017-05-17 14:54:11,749] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 14:55:57,224] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/sv/input/32d8c373-b5c8-420b-9808-8812b5501649.embl-delly_1-3-0-preFilter.20150820.somatic.sv.vcf.gz ERROR [2017-05-17 14:55:57,712] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 14:56:32,594] [TrackLoader.java:126] Loading resource, path /Users/morova/SV_data/fa49cdc9-03f2-47c7-9e78-de631400915c/32d8c373-b5c8-420b-9808-8812b5501649.dkfz-copyNumberEstimation_1-0-189.20150820.somatic.cnv.vcf ERROR [2017-05-17 14:56:32,663] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 16:33:45,310] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/sv/input/0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-05-17 16:33:45,528] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-17 19:41:17,300] [ShutdownThread.java:51] Shutting down INFO [2017-05-17 19:41:17,335] [ShutdownThread.java:51] Shutting down INFO [2017-05-18 12:42:04,569] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-18 12:42:04,570] [Main.java:136] Java 1.8.0_131 INFO [2017-05-18 12:42:04,570] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-18 12:42:04,578] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-18 12:42:04,578] [Main.java:138] OS: Mac OS X INFO [2017-05-18 12:42:06,145] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome ERROR [2017-05-18 12:42:06,426] [Main.java:199] Error checking version org.broad.igv.exceptions.HttpResponseException: Internal Server Error at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:770) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:748) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:748) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:626) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:622) at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:146) at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:139) at org.broad.igv.ui.Main$1.run(Main.java:173) at java.lang.Thread.run(Thread.java:748) INFO [2017-05-18 12:42:08,834] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-18 12:42:08,927] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-18 12:42:10,958] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/51adf6cf-f422-4d7e-aa46-cc9bf0ef8693.dkfz-copyNumberEstimation_1-0-189-hpc.1510221331.somatic.cnv.vcf ERROR [2017-05-18 12:42:11,405] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-05-18 12:42:58,539] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-05-18 12:42:58,746] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.ArithmeticException: / by zero at org.broad.igv.variant.VariantTrack.getSampleAtPosition(VariantTrack.java:947) at org.broad.igv.variant.VariantTrack.handleNameClick(VariantTrack.java:1278) at org.broad.igv.ui.panel.TrackNamePanel$NamePanelMouseAdapter.mouseClicked(TrackNamePanel.java:557) at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:269) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4534) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-05-18 14:21:08,083] [ShutdownThread.java:51] Shutting down ERROR [2017-05-18 14:21:08,088] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-05-19 17:28:58,045] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-19 17:28:58,047] [Main.java:136] Java 1.8.0_131 INFO [2017-05-19 17:28:58,047] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-19 17:28:58,057] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-19 17:28:58,057] [Main.java:138] OS: Mac OS X ERROR [2017-05-19 17:28:59,945] [Main.java:199] Error checking version org.broad.igv.exceptions.HttpResponseException: Internal Server Error at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:770) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:748) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:748) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:626) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:622) at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:146) at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:139) at org.broad.igv.ui.Main$1.run(Main.java:173) at java.lang.Thread.run(Thread.java:748) INFO [2017-05-19 17:29:00,703] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-05-19 17:29:03,603] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-05-19 17:29:03,699] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-19 17:29:18,614] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/all_TF/BEDS/TOP1.bed ERROR [2017-05-19 17:29:19,028] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-19 17:29:48,121] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/Blacklist/highconfidence_AR_250_allbinding_clean.bed ERROR [2017-05-19 17:29:48,176] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-19 17:29:57,789] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-19 17:31:31,355] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-19 17:31:33,380] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-19 17:31:34,461] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/LNCAP_Marks/TranscriptionFactor/TOP1/GSE63202_43653summitsIn64569increasedTOP1regions.bed ERROR [2017-05-19 17:31:34,586] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-19 17:42:57,815] [ShutdownThread.java:51] Shutting down ERROR [2017-05-19 17:42:57,819] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-05-24 23:11:58,498] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-24 23:11:58,499] [Main.java:136] Java 1.8.0_131 INFO [2017-05-24 23:11:58,499] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-24 23:11:58,511] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-24 23:11:58,511] [Main.java:138] OS: Mac OS X INFO [2017-05-24 23:12:00,169] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-24 23:12:02,884] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-24 23:12:02,952] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-24 23:12:07,119] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/IdentificationOfMutationSignaturesOverOVERLAPVENN/filespos/clAR_SUZ12/AR_250_allbinding_blacklistFREE.bed INFO [2017-05-24 23:12:07,212] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/IdentificationOfMutationSignaturesOverOVERLAPVENN/filespos/clAR_SUZ12/ClinicalAR_Overlap_SUZ12.bed INFO [2017-05-24 23:12:07,219] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/IdentificationOfMutationSignaturesOverOVERLAPVENN/filespos/clAR_SUZ12/Unique_SUZ12.bed ERROR [2017-05-24 23:12:07,415] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-24 23:12:28,187] [ShutdownThread.java:51] Shutting down INFO [2017-05-25 16:49:56,092] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-25 16:49:56,093] [Main.java:136] Java 1.8.0_131 INFO [2017-05-25 16:49:56,093] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-25 16:49:56,100] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-25 16:49:56,100] [Main.java:138] OS: Mac OS X INFO [2017-05-25 16:49:57,836] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-25 16:50:00,492] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-25 16:50:00,587] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-25 16:50:04,904] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/tfanalysis_LNCaP_AR/beddirectory/AR_bed/AR_250_allbinding_blacklistFREE.bed ERROR [2017-05-25 16:50:05,098] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-25 16:50:09,749] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/AR_raw_allbinding/AR_raw_allbinding_blacklistFREE.bed ERROR [2017-05-25 16:50:09,801] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-25 16:50:17,414] [ShutdownThread.java:51] Shutting down INFO [2017-05-26 23:00:46,215] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-26 23:00:46,218] [Main.java:136] Java 1.8.0_131 INFO [2017-05-26 23:00:46,218] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-26 23:00:46,225] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-26 23:00:46,225] [Main.java:138] OS: Mac OS X INFO [2017-05-26 23:00:47,935] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-26 23:00:50,990] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-26 23:00:51,074] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-26 23:01:02,766] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/ar_motif_hg19.bed ERROR [2017-05-26 23:01:03,218] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-26 23:01:52,985] [ShutdownThread.java:51] Shutting down INFO [2017-05-29 00:12:50,572] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-29 00:12:50,573] [Main.java:136] Java 1.8.0_131 INFO [2017-05-29 00:12:50,574] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-29 00:12:50,583] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-29 00:12:50,584] [Main.java:138] OS: Mac OS X INFO [2017-05-29 00:12:52,290] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg18.genome INFO [2017-05-29 00:12:54,978] [GenomeManager.java:192] Genome loaded. id= hg18 INFO [2017-05-29 00:12:55,052] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-29 00:13:14,420] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-05-29 00:13:15,880] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-05-29 00:13:18,259] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/AR_10k_allbinding/AR_10k_allbinding_blacklistFREE.bed ERROR [2017-05-29 00:13:18,355] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-29 00:13:29,283] [ShutdownThread.java:51] Shutting down INFO [2017-05-30 11:21:06,973] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-30 11:21:06,974] [Main.java:136] Java 1.8.0_131 INFO [2017-05-30 11:21:06,974] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-30 11:21:06,981] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-30 11:21:06,981] [Main.java:138] OS: Mac OS X INFO [2017-05-30 11:21:08,884] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-05-30 11:21:10,754] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-05-30 11:21:10,839] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-30 11:21:17,688] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/lncap_MethylArray/ENCFF001RIM.red.idat INFO [2017-05-30 11:21:22,828] [MessageUtils.java:74] Unknown file type: /Users/morova/Desktop/methylation/lncap_MethylArray/ENCFF001RIM.red.idat
Check file extension INFO [2017-05-30 11:21:30,462] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/lncap_MethylArray/ENCFF001RIN.green.idat INFO [2017-05-30 11:21:34,493] [MessageUtils.java:74] Unknown file type: /Users/morova/Desktop/methylation/lncap_MethylArray/ENCFF001RIN.green.idat
Check file extension ERROR [2017-05-30 11:21:35,431] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-30 11:21:51,665] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/lncap_MethylArray/ENCFF001RIM_red.idat INFO [2017-05-30 11:21:53,533] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/lncap_MethylArray/ENCFF001RIN_green.idat ERROR [2017-05-30 11:21:55,067] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-30 12:10:19,860] [ShutdownThread.java:51] Shutting down INFO [2017-05-30 12:18:36,480] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-30 12:18:36,481] [Main.java:136] Java 1.8.0_131 INFO [2017-05-30 12:18:36,482] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-30 12:18:36,487] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-30 12:18:36,488] [Main.java:138] OS: Mac OS X INFO [2017-05-30 12:18:38,270] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-05-30 12:18:40,070] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-05-30 12:18:40,148] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-30 12:18:59,895] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/AR/LNCAP_AR_methlation.bed INFO [2017-05-30 12:18:59,952] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/EZH2/EZH2_methlation.bed INFO [2017-05-30 12:19:00,022] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/SUZ12/SUZ12_methlation.bed ERROR [2017-05-30 12:19:00,037] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-30 12:19:26,232] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/SUZ12/SUZ12_methlation.bed ERROR [2017-05-30 12:19:26,727] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-30 12:20:14,120] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/hg19_cpg_island.bed ERROR [2017-05-30 12:20:14,181] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-30 13:34:53,759] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/SUZ12/SUZ12_hypermethlated_regions.bed ERROR [2017-05-30 13:34:53,887] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-30 16:49:56,921] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-05-30 17:10:55,098] [ShutdownThread.java:51] Shutting down INFO [2017-05-31 11:53:55,032] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-05-31 11:53:55,033] [Main.java:136] Java 1.8.0_131 INFO [2017-05-31 11:53:55,034] [DirectoryManager.java:72] Fetching user directory... INFO [2017-05-31 11:53:55,043] [Main.java:137] Default User Directory: /Users/morova INFO [2017-05-31 11:53:55,043] [Main.java:138] OS: Mac OS X INFO [2017-05-31 11:53:57,050] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-05-31 11:53:58,746] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-05-31 11:53:58,808] [CommandListener.java:106] Listening on port 60151 INFO [2017-05-31 11:54:37,371] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/lncap2_duke_meth.bed.gz ERROR [2017-05-31 11:54:37,409] [TrackLoader.java:275] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@2d255e70, for input source: /Users/morova/Downloads/lncap2_duke_meth.bed.gz htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@2d255e70, for input source: /Users/morova/Downloads/lncap2_duke_meth.bed.gz at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:411) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more INFO [2017-05-31 11:54:37,412] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/lncap_duke_meth.bed.gz ERROR [2017-05-31 11:54:37,418] [TrackLoader.java:275] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@1840357c, for input source: /Users/morova/Downloads/lncap_duke_meth.bed.gz htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@1840357c, for input source: /Users/morova/Downloads/lncap_duke_meth.bed.gz at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:411) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more ERROR [2017-05-31 11:54:37,421] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-31 11:54:37,422] [MessageUtils.java:74] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@2d255e70, for input source: /Users/morova/Downloads/lncap2_duke_meth.bed.gz Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@1840357c, for input source: /Users/morova/Downloads/lncap_duke_meth.bed.gz INFO [2017-05-31 11:55:22,671] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/lncap_duke_meth.bed ERROR [2017-05-31 11:55:22,683] [TrackLoader.java:275] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@729c715, for input source: /Users/morova/Downloads/lncap_duke_meth.bed htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@729c715, for input source: /Users/morova/Downloads/lncap_duke_meth.bed at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:411) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more ERROR [2017-05-31 11:55:22,686] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-31 11:55:22,686] [MessageUtils.java:74] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@729c715, for input source: /Users/morova/Downloads/lncap_duke_meth.bed INFO [2017-05-31 11:55:38,520] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/lncap2_duke_meth.bed INFO [2017-05-31 11:55:40,739] [MessageUtils.java:74] java.lang.NumberFormatException: For input string: "chr1" ERROR [2017-05-31 11:55:44,570] [TrackLoader.java:275] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@52197e14, for input source: /Users/morova/Downloads/lncap2_duke_meth.bed htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@52197e14, for input source: /Users/morova/Downloads/lncap2_duke_meth.bed at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:411) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.NumberFormatException: For input string: "chr1" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:90) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:259) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) ... 45 more ERROR [2017-05-31 11:55:44,572] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-31 11:55:44,573] [MessageUtils.java:74] Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@52197e14, for input source: /Users/morova/Downloads/lncap2_duke_meth.bed INFO [2017-05-31 12:00:41,866] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/lncap1_duke_meth.bed.gz INFO [2017-05-31 12:00:49,839] [TrackLoader.java:126] Loading resource, path /Users/morova/Downloads/lncap2_duke_meth.bed.gz ERROR [2017-05-31 12:01:00,039] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-31 12:03:48,575] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/bed-hg19/Clinical_AR_250.bed ERROR [2017-05-31 12:03:48,649] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-05-31 12:03:52,809] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/methylation/bed-hg19/SUZ12.bed ERROR [2017-05-31 12:03:52,858] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-05-31 12:04:10,949] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features7468701977060149061.tmp has inconsistent naming convention for record: ERROR [2017-05-31 12:04:10,950] [RuntimeUtils.java:97] chr18 55790667 55790668 LnCAP_R1881__GC_ 1 + 55790667 55790668 0,255,0 1 0 ERROR [2017-05-31 12:04:10,950] [RuntimeUtils.java:97] ERROR [2017-05-31 12:04:10,950] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features7468701977060149061.tmp has inconsistent naming convention for record: ERROR [2017-05-31 12:04:10,950] [RuntimeUtils.java:97] chr18 55790667 55790668 LnCAP_R1881__GC_ 1 + 55790667 55790668 0,255,0 1 0 ERROR [2017-05-31 12:04:10,950] [RuntimeUtils.java:97] ERROR [2017-05-31 12:04:26,317] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features6038515664535623307.tmp has inconsistent naming convention for record: ERROR [2017-05-31 12:04:26,318] [RuntimeUtils.java:97] chr18 55835935 55835936 LnCAP_R1881__GC_ 2 - 55835935 55835936 255,0,0 2 100 ERROR [2017-05-31 12:04:26,318] [RuntimeUtils.java:97] ERROR [2017-05-31 12:04:26,318] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features6038515664535623307.tmp has inconsistent naming convention for record: ERROR [2017-05-31 12:04:26,318] [RuntimeUtils.java:97] chr18 55835935 55835936 LnCAP_R1881__GC_ 2 - 55835935 55835936 255,0,0 2 100 ERROR [2017-05-31 12:04:26,318] [RuntimeUtils.java:97] INFO [2017-05-31 12:06:15,303] [ShutdownThread.java:51] Shutting down ERROR [2017-05-31 12:06:15,307] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-06-06 13:02:15,662] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-06 13:02:15,664] [Main.java:136] Java 1.8.0_131 INFO [2017-06-06 13:02:15,664] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-06 13:02:15,671] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-06 13:02:15,671] [Main.java:138] OS: Mac OS X INFO [2017-06-06 13:02:17,668] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-06 13:02:19,699] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-06 13:02:19,782] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-06 13:02:32,410] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/deneme2/AR_motif.bed.gz ERROR [2017-06-06 13:02:32,553] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:02:48,834] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/PWMdata/whole_vcf/AR_motif.vcf ERROR [2017-06-06 13:02:49,179] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:03:02,206] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-06 13:05:22,715] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-06-06 13:05:25,070] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-06-06 13:05:31,792] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/PWMdata/bed_pwm/AR_293_motif.bed ERROR [2017-06-06 13:05:32,071] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:05:57,426] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/SuperVCF_SNV.Prostate.vcf ERROR [2017-06-06 13:06:12,611] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:06:38,531] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-06 13:07:04,547] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-06 13:07:06,343] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-06 13:07:07,900] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/SuperVCF_SNV.Prostate.vcf ERROR [2017-06-06 13:07:14,492] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:07:20,795] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/PWMdata/bed_pwm/AR_293_motif.bed ERROR [2017-06-06 13:07:20,933] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:08:43,975] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/bgzip_GRCH37/AR_motif.bed.gz ERROR [2017-06-06 13:08:44,041] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:11:07,349] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/GRCh37/AR_motif.bed ERROR [2017-06-06 13:11:07,591] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:13:25,889] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/hg19/AR_motif.bed ERROR [2017-06-06 13:13:26,092] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:13:37,771] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/PWMdata/bed_pwm/AR_293_motif.bed ERROR [2017-06-06 13:13:38,005] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:15:09,945] [ShutdownThread.java:51] Shutting down INFO [2017-06-06 13:24:20,899] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-06 13:24:20,900] [Main.java:136] Java 1.8.0_131 INFO [2017-06-06 13:24:20,900] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-06 13:24:20,908] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-06 13:24:20,908] [Main.java:138] OS: Mac OS X INFO [2017-06-06 13:24:22,618] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-06 13:24:24,592] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-06 13:24:24,667] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-06 13:24:26,436] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/PWMdata/whole_vcf/AR_motif.vcf ERROR [2017-06-06 13:24:26,733] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:24:35,234] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/bgzip_GRCH37/AR_293_motif.bed.gz ERROR [2017-06-06 13:24:35,285] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:24:54,564] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/hg19/AR_293_motif.bed ERROR [2017-06-06 13:24:54,933] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:25:15,515] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/PWMdata/bed_pwm/hg19/AR_motif_hg19.bed ERROR [2017-06-06 13:25:15,670] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 13:25:33,622] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-06 14:41:54,383] [ShutdownThread.java:51] Shutting down INFO [2017-06-06 14:41:54,399] [ShutdownThread.java:51] Shutting down INFO [2017-06-06 17:53:46,615] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-06 17:53:46,616] [Main.java:136] Java 1.8.0_131 INFO [2017-06-06 17:53:46,616] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-06 17:53:46,624] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-06 17:53:46,624] [Main.java:138] OS: Mac OS X INFO [2017-06-06 17:53:48,105] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-06 17:53:49,811] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-06 17:53:49,899] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-06 17:53:52,114] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/GRCh37/SUZ12.bed ERROR [2017-06-06 17:53:52,250] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 17:54:06,917] [ShutdownThread.java:51] Shutting down INFO [2017-06-06 18:33:52,736] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-06 18:33:52,737] [Main.java:136] Java 1.8.0_131 INFO [2017-06-06 18:33:52,737] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-06 18:33:52,746] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-06 18:33:52,746] [Main.java:138] OS: Mac OS X INFO [2017-06-06 18:33:54,430] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-06 18:33:56,101] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-06 18:33:56,183] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-06 18:34:01,168] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/LNCAP_Marks/TranscriptionFactor/AR/GSE83860_GSM2219854_ChIPseq_LNCaP_AR_DHT_sorted.bed ERROR [2017-06-06 18:34:01,384] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 18:34:05,440] [TrackLoader.java:126] Loading resource, path /Users/morova/Dropbox/ProsatateCancer_TF_database/LNCAP_Marks/TranscriptionFactor/AR/LNCaP_AR_R1881.bigWig ERROR [2017-06-06 18:34:05,576] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 22:31:06,166] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/LNCaP_AR/LNCaP_AR_r1881.bed ERROR [2017-06-06 22:31:06,489] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 23:12:46,543] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/LNCaP_AR/cucuk.bed ERROR [2017-06-06 23:12:46,803] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-06 23:12:58,975] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-07 01:09:15,243] [ShutdownThread.java:51] Shutting down INFO [2017-06-07 23:09:34,593] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-07 23:09:34,595] [Main.java:136] Java 1.8.0_131 INFO [2017-06-07 23:09:34,595] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-07 23:09:34,610] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-07 23:09:34,610] [Main.java:138] OS: Mac OS X INFO [2017-06-07 23:09:36,699] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-07 23:09:38,929] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-07 23:09:38,996] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-07 23:09:55,159] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-816e-e3e4-e050-11ac0c4860c5.dkfz-copyNumberEstimation_1-0-189-hpc.1602082116.somatic.cnv.vcf INFO [2017-06-07 23:09:55,626] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-7343-fdd0-e050-11ac0c484cab.dkfz-copyNumberEstimation_1-0-189-hpc.1602082143.somatic.cnv.vcf INFO [2017-06-07 23:09:55,779] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-7344-fdd0-e050-11ac0c484cab.dkfz-copyNumberEstimation_1-0-189-hpc.1602082116.somatic.cnv.vcf INFO [2017-06-07 23:09:56,037] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-7346-fdd0-e050-11ac0c484cab.dkfz-copyNumberEstimation_1-0-189-hpc.1602082130.somatic.cnv.vcf ERROR [2017-06-07 23:09:56,100] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-07 23:38:49,197] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz ERROR [2017-06-07 23:38:49,212] [TrackLoader.java:275] java.io.EOFException at java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:268) at java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:258) at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:164) at java.util.zip.GZIPInputStream.(GZIPInputStream.java:79) at java.util.zip.GZIPInputStream.(GZIPInputStream.java:91) at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:122) at org.broad.igv.util.ParsingUtils.openAsciiReader(ParsingUtils.java:90) at org.broad.igv.data.expression.ExpressionFileParser.parsableMAGE_TAB(ExpressionFileParser.java:134) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:213) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-06-07 23:38:49,217] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-07 23:41:14,103] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz INFO [2017-06-07 23:48:49,878] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-07 23:48:49,879] [Main.java:136] Java 1.8.0_131 INFO [2017-06-07 23:48:49,879] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-07 23:48:49,886] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-07 23:48:49,886] [Main.java:138] OS: Mac OS X INFO [2017-06-07 23:48:51,473] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-07 23:48:53,063] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-07 23:48:53,143] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-07 23:59:12,848] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz INFO [2017-06-08 00:04:33,409] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-08 00:04:33,418] [Main.java:136] Java 1.8.0_131 INFO [2017-06-08 00:04:33,418] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-08 00:04:33,421] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-08 00:04:33,422] [Main.java:138] OS: Mac OS X INFO [2017-06-08 00:04:35,714] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-08 00:04:37,569] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-08 00:04:37,632] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-08 00:04:57,227] [TrackLoader.java:126] Loading resource, path /Users/morova/subsetted.vcf ERROR [2017-06-08 00:04:57,428] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 00:05:44,965] [ShutdownThread.java:51] Shutting down INFO [2017-06-08 00:05:44,968] [ShutdownThread.java:51] Shutting down INFO [2017-06-08 15:11:54,365] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-08 15:11:54,366] [Main.java:136] Java 1.8.0_131 INFO [2017-06-08 15:11:54,366] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-08 15:11:54,393] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-08 15:11:54,394] [Main.java:138] OS: Mac OS X INFO [2017-06-08 15:11:56,082] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-08 15:11:57,641] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-08 15:11:57,713] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-08 15:14:54,526] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.dkfz-copyNumberEstimation_1-0-189.20151029.somatic.cnv.vcf INFO [2017-06-08 15:14:54,900] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bd3a230-531e-44aa-9999-b8ed8da0176b.dkfz-copyNumberEstimation_1-0-189-hpc.1602261554.somatic.cnv.vcf INFO [2017-06-08 15:14:54,948] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-7ed6-9ccc-e050-11ac0c481957.dkfz-copyNumberEstimation_1-0-189-hpc.1602082145.somatic.cnv.vcf INFO [2017-06-08 15:14:55,003] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-816e-e3e4-e050-11ac0c4860c5.dkfz-copyNumberEstimation_1-0-189-hpc.1602082116.somatic.cnv.vcf INFO [2017-06-08 15:14:55,252] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-7343-fdd0-e050-11ac0c484cab.dkfz-copyNumberEstimation_1-0-189-hpc.1602082143.somatic.cnv.vcf INFO [2017-06-08 15:14:55,340] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-7344-fdd0-e050-11ac0c484cab.dkfz-copyNumberEstimation_1-0-189-hpc.1602082116.somatic.cnv.vcf INFO [2017-06-08 15:14:55,445] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-7346-fdd0-e050-11ac0c484cab.dkfz-copyNumberEstimation_1-0-189-hpc.1602082130.somatic.cnv.vcf INFO [2017-06-08 15:14:55,474] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-8170-e3e4-e050-11ac0c4860c5.dkfz-copyNumberEstimation_1-0-189-hpc.1602082116.somatic.cnv.vcf INFO [2017-06-08 15:14:55,493] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-8172-e3e4-e050-11ac0c4860c5.dkfz-copyNumberEstimation_1-0-189-hpc.1602082145.somatic.cnv.vcf INFO [2017-06-08 15:14:55,539] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-8173-e3e4-e050-11ac0c4860c5.dkfz-copyNumberEstimation_1-0-189-hpc.1602082144.somatic.cnv.vcf INFO [2017-06-08 15:14:55,606] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-8175-e3e4-e050-11ac0c4860c5.dkfz-copyNumberEstimation_1-0-189-hpc.1602082116.somatic.cnv.vcf INFO [2017-06-08 15:14:55,637] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1043-8187-e3e4-e050-11ac0c4860c5.dkfz-copyNumberEstimation_1-0-189-hpc.1602082116.somatic.cnv.vcf INFO [2017-06-08 15:14:55,665] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_CNV_PCA/input/0bfd1068-3fc3-a95b-e050-11ac0c4860c3.dkfz-copyNumberEstimation_1-0-189-hpc.1602082128.somatic.cnv.vcf ERROR [2017-06-08 15:14:55,721] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 15:16:09,848] [ShutdownThread.java:51] Shutting down INFO [2017-06-08 15:16:25,567] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-08 15:16:25,568] [Main.java:136] Java 1.8.0_131 INFO [2017-06-08 15:16:25,568] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-08 15:16:25,571] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-08 15:16:25,571] [Main.java:138] OS: Mac OS X INFO [2017-06-08 15:16:26,876] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-08 15:16:28,499] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-08 15:16:28,568] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-08 15:16:34,863] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf ERROR [2017-06-08 15:16:35,273] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 121: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 121: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,282] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bd3a230-531e-44aa-9999-b8ed8da0176b.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,290] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 39: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bd3a230-531e-44aa-9999-b8ed8da0176b.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 39: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bd3a230-531e-44aa-9999-b8ed8da0176b.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,294] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,311] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 54: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 54: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,314] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-816e-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,337] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 92: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-816e-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-816e-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,338] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7343-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,397] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 204: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7343-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 204: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7343-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,398] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,438] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 103: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 103: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,439] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,447] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 63: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 63: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,448] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,456] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 59: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 59: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,457] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8172-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,469] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 64: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8172-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 64: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8172-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,470] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8173-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,478] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 63: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8173-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 63: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8173-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:35,479] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8175-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:35,486] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 64: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8175-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 64: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8175-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-06-08 15:16:35,489] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 15:16:35,491] [MessageUtils.java:74] The provided VCF file is malformed at approximately line number 121: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf The provided VCF file is malformed at approximately line number 39: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bd3a230-531e-44aa-9999-b8ed8da0176b.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 54: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 92: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-816e-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 204: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7343-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 103: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 63: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 59: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 64: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8172-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 63: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8173-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 64: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8175-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf INFO [2017-06-08 15:16:43,909] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8187-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:43,923] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 108: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8187-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 108: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8187-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-06-08 15:16:43,925] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 15:16:43,925] [MessageUtils.java:74] The provided VCF file is malformed at approximately line number 108: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/input/0bfd1043-8187-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf INFO [2017-06-08 15:16:52,521] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf ERROR [2017-06-08 15:16:52,570] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 38: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 38: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.(TribbleIndexedFeatureReader.java:309) at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276) at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:304) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:52,571] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0bd3a230-531e-44aa-9999-b8ed8da0176b.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf INFO [2017-06-08 15:16:52,588] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:52,605] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 65: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 65: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:52,611] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-816e-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf INFO [2017-06-08 15:16:52,620] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7343-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf INFO [2017-06-08 15:16:52,640] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:52,647] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 40: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 40: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:52,648] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:52,658] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 65: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 65: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-08 15:16:52,770] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf ERROR [2017-06-08 15:16:52,773] [TrackLoader.java:275] The provided VCF file is malformed at approximately line number 42: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 42: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:784) at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:569) at htsjdk.variant.vcf.AbstractVCFCodec.parseSingleAltAllele(AbstractVCFCodec.java:609) at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:536) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69) at org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadVCF(TrackLoader.java:324) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:408) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-06-08 15:16:52,775] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 15:16:52,775] [MessageUtils.java:74] The provided VCF file is malformed at approximately line number 38: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0a6be23a-d5a0-4e95-ada2-a61b2b5d9485.embl-delly_1-3-0-preFilter.20151029.somatic.sv.vcf The provided VCF file is malformed at approximately line number 65: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7ed6-9ccc-e050-11ac0c481957.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 40: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7344-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 65: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-7346-fdd0-e050-11ac0c484cab.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf The provided VCF file is malformed at approximately line number 42: unparsable vcf record with allele BND, for input source: /Volumes/blackhole/all_SV_PCA/final/final.0bfd1043-8170-e3e4-e050-11ac0c4860c5.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf INFO [2017-06-08 15:17:14,555] [ShutdownThread.java:51] Shutting down ERROR [2017-06-08 15:17:14,556] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64) INFO [2017-06-08 23:10:20,894] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-08 23:10:20,895] [Main.java:136] Java 1.8.0_131 INFO [2017-06-08 23:10:20,895] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-08 23:10:20,901] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-08 23:10:20,901] [Main.java:138] OS: Mac OS X INFO [2017-06-08 23:10:22,432] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-08 23:10:24,151] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-08 23:10:24,214] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-08 23:10:58,873] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/CpG.bed.gz ERROR [2017-06-08 23:10:59,820] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 23:11:16,689] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-08 23:36:17,778] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/CpG.bed.gz ERROR [2017-06-08 23:36:18,009] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 23:43:06,986] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/sorted_deneme3.bed.gz ERROR [2017-06-08 23:43:07,381] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-08 23:56:57,533] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/CpG.bed.gz ERROR [2017-06-08 23:56:57,652] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 00:00:13,823] [ShutdownThread.java:51] Shutting down INFO [2017-06-09 00:00:13,831] [ShutdownThread.java:51] Shutting down INFO [2017-06-09 10:24:14,136] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-09 10:24:14,137] [Main.java:136] Java 1.8.0_131 INFO [2017-06-09 10:24:14,137] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-09 10:24:14,149] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-09 10:24:14,149] [Main.java:138] OS: Mac OS X INFO [2017-06-09 10:24:16,152] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-09 10:24:18,064] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-09 10:24:18,156] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-09 10:25:05,436] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/CpG.bed.gz ERROR [2017-06-09 10:25:05,891] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 10:25:26,604] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/highconfidence_LNCaP_Mehtylation.bed ERROR [2017-06-09 10:25:31,293] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 10:25:55,112] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-09 10:57:22,342] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/sorted_deneme3.bed.gz ERROR [2017-06-09 10:57:22,600] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 11:02:17,393] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/CpG.bed.gz ERROR [2017-06-09 11:02:17,610] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 11:18:06,788] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/CpG.bed.gz ERROR [2017-06-09 11:18:07,056] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 11:45:00,472] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/new_one/CpG_methylation_status.bed INFO [2017-06-09 11:51:44,151] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-09 11:51:44,159] [Main.java:136] Java 1.8.0_131 INFO [2017-06-09 11:51:44,159] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-09 11:51:44,167] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-09 11:51:44,168] [Main.java:138] OS: Mac OS X INFO [2017-06-09 11:51:45,785] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-09 11:51:47,707] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-09 11:51:47,796] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-09 11:53:48,753] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/new_one/CpG_methylation_status.bed.gz ERROR [2017-06-09 11:53:52,186] [TrackLoader.java:275] java.io.EOFException: Unexpected end of ZLIB input stream htsjdk.samtools.util.RuntimeIOException: java.io.EOFException: Unexpected end of ZLIB input stream at htsjdk.tribble.readers.LineReaderUtil$2.readLine(LineReaderUtil.java:80) at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:24) at htsjdk.tribble.readers.LineIteratorImpl.advance(LineIteratorImpl.java:11) at htsjdk.samtools.util.AbstractIterator.next(AbstractIterator.java:57) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:411) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.io.EOFException: Unexpected end of ZLIB input stream at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240) at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158) at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117) at java.io.FilterInputStream.read(FilterInputStream.java:107) at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:127) at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:79) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at htsjdk.tribble.readers.LongLineBufferedReader.fill(LongLineBufferedReader.java:140) at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:298) at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:354) at htsjdk.tribble.readers.LineReaderUtil$2.readLine(LineReaderUtil.java:78) ... 50 more ERROR [2017-06-09 11:53:52,191] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 11:53:52,193] [MessageUtils.java:74] java.io.EOFException: Unexpected end of ZLIB input stream INFO [2017-06-09 11:55:11,727] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/new_one/CpG_methylation_status.bed.gz ERROR [2017-06-09 12:00:56,082] [TrackLoader.java:275] java.lang.NullPointerException at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:260) at org.broad.igv.feature.tribble.IGVBEDCodec.decode(IGVBEDCodec.java:51) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79) at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:321) at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.next(TribbleIndexedFeatureReader.java:282) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:306) at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.(TribbleFeatureSource.java:287) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:411) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-06-09 12:00:56,341] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 12:16:09,681] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/new_one/lolo.bed ERROR [2017-06-09 12:16:25,910] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 12:16:52,610] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/CpG.bed.gz ERROR [2017-06-09 12:16:53,288] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 12:17:14,840] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/highconfidence_LNCaP_Mehtylation.bed ERROR [2017-06-09 12:17:24,320] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 12:17:55,924] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-09 12:19:28,838] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/methylated.bed ERROR [2017-06-09 12:19:31,998] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 13:02:27,087] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/LNCaP_CpG_statust_noNAN.bed ERROR [2017-06-09 13:02:58,707] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 13:55:32,879] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/hg19/Clinical_AR_250.bed ERROR [2017-06-09 13:55:32,962] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 14:15:56,006] [ShutdownThread.java:51] Shutting down INFO [2017-06-09 14:15:56,154] [ShutdownThread.java:51] Shutting down INFO [2017-06-09 14:57:48,430] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-09 14:57:48,431] [Main.java:136] Java 1.8.0_131 INFO [2017-06-09 14:57:48,432] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-09 14:57:48,438] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-09 14:57:48,438] [Main.java:138] OS: Mac OS X INFO [2017-06-09 14:57:49,983] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-09 14:57:51,669] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-09 14:57:51,763] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-09 14:57:59,471] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/CpG.bed ERROR [2017-06-09 14:58:02,394] [TrackLoader.java:275] An index is required, but none found., for input source: /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/CpG.bed htsjdk.tribble.TribbleException: An index is required, but none found., for input source: /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/CpG.bed at htsjdk.tribble.TribbleIndexedFeatureReader.(TribbleIndexedFeatureReader.java:111) at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:89) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:91) at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69) at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:411) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:236) at org.broad.igv.ui.IGV.load(IGV.java:1809) at org.broad.igv.ui.IGV.load(IGV.java:1846) at org.broad.igv.ui.panel.DataPanelContainer$FileDropTargetListener.drop(DataPanelContainer.java:202) at java.awt.dnd.DropTarget.drop(DropTarget.java:455) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538) at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-06-09 14:58:02,400] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 14:58:02,402] [MessageUtils.java:74] An index is required, but none found., for input source: /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/CpG.bed INFO [2017-06-09 14:58:07,254] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/CpG.bed.gz ERROR [2017-06-09 14:58:07,613] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 14:58:29,644] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/highconfidence_LNCaP_Mehtylation.bed ERROR [2017-06-09 14:58:34,453] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 14:59:10,858] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/hg19/AR.bed ERROR [2017-06-09 14:59:11,015] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-09 15:00:22,301] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-09 18:55:08,388] [ShutdownThread.java:51] Shutting down INFO [2017-06-09 18:55:08,414] [ShutdownThread.java:51] Shutting down INFO [2017-06-11 19:40:58,847] [Main.java:135] Startup IGV Version 2.3.93 (151)05/15/2017 06:11 PM INFO [2017-06-11 19:40:58,848] [Main.java:136] Java 1.8.0_131 INFO [2017-06-11 19:40:58,849] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-11 19:40:58,861] [Main.java:137] Default User Directory: /Users/morova INFO [2017-06-11 19:40:58,861] [Main.java:138] OS: Mac OS X INFO [2017-06-11 19:41:00,687] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-11 19:41:02,702] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-11 19:41:02,771] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-11 19:41:55,929] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/SuperVCF_SNV.Prostate.vcf.gz ERROR [2017-06-11 19:41:56,248] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-11 19:42:18,119] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/CpG.bed.gz ERROR [2017-06-11 19:42:18,260] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-06-11 19:43:53,659] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features2380657987786881193.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:43:53,661] [RuntimeUtils.java:97] 12 67099340 67099341 ERROR [2017-06-11 19:43:53,661] [RuntimeUtils.java:97] ERROR [2017-06-11 19:43:53,661] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features2380657987786881193.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:43:53,661] [RuntimeUtils.java:97] 12 67099340 67099341 ERROR [2017-06-11 19:43:53,662] [RuntimeUtils.java:97] ERROR [2017-06-11 19:44:22,063] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features1607724569042701858.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:44:22,070] [RuntimeUtils.java:97] 8 172094 172095 ERROR [2017-06-11 19:44:22,071] [RuntimeUtils.java:97] ERROR [2017-06-11 19:44:22,112] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features1607724569042701858.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:44:22,112] [RuntimeUtils.java:97] 8 172094 172095 ERROR [2017-06-11 19:44:22,112] [RuntimeUtils.java:97] ERROR [2017-06-11 19:45:02,683] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features5262883856877935328.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:45:02,683] [RuntimeUtils.java:97] 19 252259 252260 ERROR [2017-06-11 19:45:02,683] [RuntimeUtils.java:97] ERROR [2017-06-11 19:45:02,695] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features5262883856877935328.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:45:02,695] [RuntimeUtils.java:97] 19 252259 252260 ERROR [2017-06-11 19:45:02,695] [RuntimeUtils.java:97] ERROR [2017-06-11 19:45:44,795] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features6011346719156129719.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:45:44,803] [RuntimeUtils.java:97] 7 40469 40470 ERROR [2017-06-11 19:45:44,803] [RuntimeUtils.java:97] ERROR [2017-06-11 19:45:44,866] [RuntimeUtils.java:97] ***** WARNING: File /var/folders/wr/n0pp081s4698_kzdfkstv9w80000gn/T/features6011346719156129719.tmp has inconsistent naming convention for record: ERROR [2017-06-11 19:45:44,867] [RuntimeUtils.java:97] 7 40469 40470 ERROR [2017-06-11 19:45:44,867] [RuntimeUtils.java:97] INFO [2017-06-11 23:36:38,986] [ShutdownThread.java:51] Shutting down INFO [2017-06-11 23:36:39,035] [ShutdownThread.java:51] Shutting down INFO [2017-06-12 10:39:47,767] [Main.java:150] Startup IGV Version 2.3.94 (152)06/11/2017 07:09 PM INFO [2017-06-12 10:39:47,768] [Main.java:151] Java 1.8.0_131 INFO [2017-06-12 10:39:47,768] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-12 10:39:47,778] [Main.java:152] Default User Directory: /Users/morova INFO [2017-06-12 10:39:47,779] [Main.java:153] OS: Mac OS X INFO [2017-06-12 10:39:49,973] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/b37.genome INFO [2017-06-12 10:39:51,976] [GenomeManager.java:192] Genome loaded. id= b37 INFO [2017-06-12 10:39:52,081] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-12 10:41:21,923] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/hg19CpG/CpG.bed.gz ERROR [2017-06-12 10:41:22,158] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-12 10:41:55,296] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/ENCFF001TON.bed ERROR [2017-06-12 10:42:02,242] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-12 10:43:02,492] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/highconfidence_LNCaP_Mehtylation.bed ERROR [2017-06-12 10:43:09,021] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-12 11:38:08,459] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/Methylation_RRRE/GSE86832/LNCaP_WGBS.bed.gz ERROR [2017-06-12 11:38:08,955] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-12 11:38:12,373] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-12 14:08:06,314] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/hg19/H3K36me3.bed ERROR [2017-06-12 14:08:12,050] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-12 14:36:33,395] [ShutdownThread.java:51] Shutting down INFO [2017-06-12 14:36:33,648] [ShutdownThread.java:51] Shutting down INFO [2017-06-14 10:14:23,852] [Main.java:150] Startup IGV Version 2.3.94 (152)06/11/2017 07:09 PM INFO [2017-06-14 10:14:23,855] [Main.java:151] Java 1.8.0_131 INFO [2017-06-14 10:14:23,855] [DirectoryManager.java:72] Fetching user directory... INFO [2017-06-14 10:14:23,863] [Main.java:152] Default User Directory: /Users/morova INFO [2017-06-14 10:14:23,863] [Main.java:153] OS: Mac OS X INFO [2017-06-14 10:14:25,707] [GenomeManager.java:145] Loading genome: /Users/morova/igv/genomes/hg19.genome INFO [2017-06-14 10:14:28,106] [GenomeManager.java:192] Genome loaded. id= hg19 INFO [2017-06-14 10:14:28,191] [CommandListener.java:106] Listening on port 60151 INFO [2017-06-14 10:14:46,359] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/Methylation_RRRE/GSE86832/LNCaP/LNCaP_WGBS.bed.gz ERROR [2017-06-14 10:14:47,281] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 10:18:38,456] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/highconfidence_LNCaP_Mehtylation.bed ERROR [2017-06-14 10:18:43,580] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 10:19:00,608] [HttpUtils.java:856] Range-byte request succeeded INFO [2017-06-14 10:22:55,260] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/GenomeFasta/hg19/hg19bychromosome/bedfiles/hg19CpG/CpG.bed.gz ERROR [2017-06-14 10:22:55,414] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 11:03:03,379] [MessageUtils.java:74] Cannot find feature or locus: 14227856 INFO [2017-06-14 11:04:28,311] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_296926 INFO [2017-06-14 11:04:33,597] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_296926 INFO [2017-06-14 11:04:38,848] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_296926 INFO [2017-06-14 11:04:47,735] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_298511 INFO [2017-06-14 11:05:28,511] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_298522 INFO [2017-06-14 11:05:38,723] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_298698 INFO [2017-06-14 11:05:48,358] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/Methylation_RRRE/GSE86832/LNCaP/LNCaP_WGBS.bed.gz ERROR [2017-06-14 11:05:48,835] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 11:05:50,448] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_298698 INFO [2017-06-14 11:06:11,698] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_298698 INFO [2017-06-14 11:07:35,674] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_2985222 INFO [2017-06-14 11:13:01,606] [MessageUtils.java:74] Cannot find feature or locus: ILNCaP_WGBS_2985222 INFO [2017-06-14 11:13:11,401] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_2985222 INFO [2017-06-14 11:13:34,238] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_2985222 INFO [2017-06-14 11:17:12,958] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/Methylation_RRRE/GSE86832/LNCaP/LNCaP_WGBS.bed.gz ERROR [2017-06-14 11:17:13,592] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 11:17:16,061] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_2985222 INFO [2017-06-14 11:17:21,227] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/Methylation_RRRE/GSE86832/LNCaP/LNCaP_WGBS.bed ERROR [2017-06-14 11:19:39,791] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 11:19:42,362] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_2985222 INFO [2017-06-14 11:19:55,051] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_2985221 INFO [2017-06-14 11:20:01,255] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_2985221 INFO [2017-06-14 11:20:12,228] [MessageUtils.java:74] Cannot find feature or locus: CpG_13428635 INFO [2017-06-14 11:20:24,091] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/highconf_250wider.bed ERROR [2017-06-14 11:20:24,209] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 11:24:06,303] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/Blacklist/highconfidence_AR_250_allbinding_clean.bed ERROR [2017-06-14 11:24:06,357] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 11:24:14,244] [MessageUtils.java:74] Cannot find feature or locus: peakno_!101 INFO [2017-06-14 11:26:02,107] [TrackLoader.java:126] Loading resource, path /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/PCA_ICGC/Blacklist/deneme1.bed.gz ERROR [2017-06-14 11:26:02,153] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String ERROR [2017-06-14 11:26:15,500] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.track.TrackMenuUtils$14.actionPerformed(TrackMenuUtils.java:692) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ERROR [2017-06-14 11:27:07,387] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.track.TrackMenuUtils$14.actionPerformed(TrackMenuUtils.java:692) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuItemUI.java:943) at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:586) at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:483) at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:429) at javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:329) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:879) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-14 11:27:24,481] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_20721247 INFO [2017-06-14 11:28:16,574] [IGV.java:1701] Loading 1 resources. INFO [2017-06-14 11:28:16,583] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/Methylation_RRRE/GSE86832/LNCaP/LNCaP_WGBS.bed.gz INFO [2017-06-14 11:28:28,863] [MessageUtils.java:74] Cannot find feature or locus: LNCaP_WGBS_20721247 INFO [2017-06-14 11:35:17,574] [MessageUtils.java:74] Cannot find feature or locus: CpG_120213 INFO [2017-06-14 11:35:22,111] [MessageUtils.java:74] Cannot find feature or locus: CpG_100 INFO [2017-06-14 11:35:24,249] [MessageUtils.java:74] Cannot find feature or locus: CpG_1000 ERROR [2017-06-14 11:36:41,638] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.NullPointerException at org.broad.igv.track.TrackMenuUtils$14.actionPerformed(TrackMenuUtils.java:692) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) INFO [2017-06-14 11:37:57,290] [MessageUtils.java:74] Cannot find feature or locus: CpG_1101 INFO [2017-06-14 11:39:13,318] [TrackLoader.java:126] Loading resource, path /Volumes/blackhole/Methylation_RRRE/GSE86832/LNCaP/lolo.bed ERROR [2017-06-14 11:39:13,369] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 11:41:15,715] [MessageUtils.java:74] Cannot find feature or locus: CpG_1000 INFO [2017-06-14 12:06:12,823] [TrackLoader.java:126] Loading resource, path /Users/morova/Desktop/TF_database_query/Methylation/sorted_formatted_highconfidence_LNCaP_Methylation.bed ERROR [2017-06-14 12:06:27,007] [DataPanelContainer.java:223] java.awt.datatransfer.UnsupportedFlavorException: Unicode String INFO [2017-06-14 13:09:50,293] [ShutdownThread.java:51] Shutting down ERROR [2017-06-14 13:09:50,320] [DefaultExceptionHandler.java:49] Unhandled exception java.lang.IllegalStateException: zip file closed at java.util.zip.ZipFile.ensureOpen(ZipFile.java:669) at java.util.zip.ZipFile.getEntry(ZipFile.java:309) at java.util.jar.JarFile.getEntry(JarFile.java:240) at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source) at java.util.jar.JarFile.getJarEntry(JarFile.java:223) at com.sun.deploy.security.DeployURLClassPath$JarLoader.getResource(Unknown Source) at com.sun.deploy.security.DeployURLClassPath.getResource(Unknown Source) at java.net.URLClassLoader$1.run(URLClassLoader.java:365) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at com.sun.jnlp.JNLPClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:411) at com.sun.jnlp.JNLPClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:52) at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)