A user mentioned an issue that IGB was having with making a track from a threshold of a bedgraph file. When the user clicks Make Track, IGB never finishes making the track.

When Nowlan tried to do the same thing it didn't freeze, but it did create several errors (in the attached stack trace), followed by producing a track with no information. When he tried making the track over and over, at different zoom levels, it eventually started working.

To reproduce in IGB 8.3.4 (not yet tested on 8.4.0):

1. Download the bedgraph file (CHG–OT Bedgraph BS-seq Chr1 KO) at the following link: https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature
2. Load the bedgraph file onto chr1 of Arabidopsis. Load the data for the entire chromosome.
3. Click on the bedgraph track, and under the graph tab select thresholding.
4. Change the values of thresholding to: By Value = 70, Max Gap = 10, Min Run = 1 (these are the values I used in the focus on a feature previously with no issue).
5. Click Make track (still at the level of the whole chromosome) - when I did this IGB made a new track, but there was nothing in it.
6. Zoom in to the level of base pairs and try to Make a track from the thresholding again.
7. Zoom back out to the whole chromosome and try to make a track again – eventually IGB should make a track, or at least in my case it did after some amount of repeating.

See below for the exception generated during this testing:

09:38:26.262 INFO com.affymetrix.igb.IGB - Starting: Integrated Genome Browser 8.3.4
09:38:26.264 INFO com.affymetrix.igb.IGB - Java version: 1.8.0_40 from Oracle Corporation
09:38:26.266 INFO com.affymetrix.igb.IGB - System memory: 3.8 GB
09:38:27.886 ERROR c.a.i.bookmarks.SimpleBookmarkServer - Couldn't find an available port for IGB to listen to control requests on port 7085!
Turning off IGB's URL-based control features
09:38:27.926 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file /Users/lorainelab/.igb/bookmarks.html
09:38:27.932 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file /Users/lorainelab/.igb/bookmarks.html~
09:38:27.958 INFO c.a.genometry.util.LocalUrlCacher - Synonyms found at: http://igbquickload.org/quickload/synonyms.txt
09:38:28.820 INFO com.affymetrix.igb.Activator - IGB Started
09:38:29.056 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework
09:38:29.056 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common
09:38:29.056 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab
09:38:29.056 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library
09:38:29.056 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler
09:38:29.056 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler
09:38:29.057 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: BigWig
09:38:29.057 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark
09:38:29.057 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.codec
09:38:29.057 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.compress
09:38:29.057 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.csv
09:38:29.057 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.io
09:38:29.058 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3
09:38:29.058 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool
09:38:29.058 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-gui
09:38:29.058 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView
09:38:29.058 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry
09:38:29.058 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz
09:38:29.058 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab
09:38:29.059 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava
09:38:29.059 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor
09:38:29.059 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb
09:38:29.059 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions-api
09:38:29.059 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services-api
09:38:29.059 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript
09:38:29.059 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt
09:38:29.060 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate
09:38:29.060 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch
09:38:29.060 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic
09:38:29.060 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core
09:38:29.060 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.logging-config
09:38:29.060 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast
09:38:29.061 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr
09:38:29.061 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor
09:38:29.061 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: pluginsPage
09:38:29.061 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView
09:38:29.061 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites
09:38:29.062 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModeLucene
09:38:29.062 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps
09:38:29.062 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView
09:38:29.062 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer
09:38:29.062 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper
09:38:29.062 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api
09:38:29.063 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey
09:38:29.063 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding
09:38:29.063 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: tutorial
09:38:29.063 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update
09:38:29.063 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service
09:38:29.063 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: windowsServiceDef
09:38:29.064 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 4.2.1.p1
09:39:17.985 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 0.749 secs
09:39:47.466 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 0.002 secs
09:39:48.597 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 0.002 secs
09:39:58.229 WARN c.a.g.util.SelectionInfoUtils - Sym class not handled: CompositeGraphSym
09:39:58.236 WARN c.a.g.util.SelectionInfoUtils - Sym class not handled: CompositeGraphSym
09:40:20.547 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 0.003 secs
Jun 03, 2015 9:40:21 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: -87878
java.lang.ArrayIndexOutOfBoundsException: -87878
at com.affymetrix.genometry.symmetry.impl.GraphSym.getGraphWidthCoord(GraphSym.java:346)
at com.affymetrix.igb.shared.GraphGlyph.drawThresholdedRegions(GraphGlyph.java:955)
at com.affymetrix.igb.thresholding.ThresholdOperator.operate(ThresholdOperator.java:44)
at com.affymetrix.genometry.symloader.Delegate.getRegion(Delegate.java:111)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:155)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:131)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:111)
at com.affymetrix.genometry.symloader.Delegate.loadFeatures(Delegate.java:185)
at com.affymetrix.genometry.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:106)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:956)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:888)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:883)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

java.lang.ArrayIndexOutOfBoundsException: -87878
at com.affymetrix.genometry.symmetry.impl.GraphSym.getGraphWidthCoord(GraphSym.java:346)
at com.affymetrix.igb.shared.GraphGlyph.drawThresholdedRegions(GraphGlyph.java:955)
at com.affymetrix.igb.thresholding.ThresholdOperator.operate(ThresholdOperator.java:44)
at com.affymetrix.genometry.symloader.Delegate.getRegion(Delegate.java:111)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:155)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:131)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:111)
at com.affymetrix.genometry.symloader.Delegate.loadFeatures(Delegate.java:185)
at com.affymetrix.genometry.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:106)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:956)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:888)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:883)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
09:40:58.162 WARN c.a.g.util.SelectionInfoUtils - Sym class not handled: CompositeGraphSym
09:41:01.058 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 0.003 secs
Jun 03, 2015 9:41:01 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: -240055
java.lang.ArrayIndexOutOfBoundsException: -240055
at com.affymetrix.genometry.symmetry.impl.GraphSym.getGraphWidthCoord(GraphSym.java:346)
at com.affymetrix.igb.shared.GraphGlyph.drawThresholdedRegions(GraphGlyph.java:955)
at com.affymetrix.igb.thresholding.ThresholdOperator.operate(ThresholdOperator.java:44)
at com.affymetrix.genometry.symloader.Delegate.getRegion(Delegate.java:111)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:155)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:131)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:111)
at com.affymetrix.genometry.symloader.Delegate.loadFeatures(Delegate.java:185)
at com.affymetrix.genometry.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:106)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:956)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:888)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:883)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

java.lang.ArrayIndexOutOfBoundsException: -240055
at com.affymetrix.genometry.symmetry.impl.GraphSym.getGraphWidthCoord(GraphSym.java:346)
at com.affymetrix.igb.shared.GraphGlyph.drawThresholdedRegions(GraphGlyph.java:955)
at com.affymetrix.igb.thresholding.ThresholdOperator.operate(ThresholdOperator.java:44)
at com.affymetrix.genometry.symloader.Delegate.getRegion(Delegate.java:111)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:155)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:131)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:111)
at com.affymetrix.genometry.symloader.Delegate.loadFeatures(Delegate.java:185)
at com.affymetrix.genometry.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:106)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:956)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:888)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:883)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:69)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
09:41:18.922 WARN c.a.g.util.SelectionInfoUtils - Sym class not handled: CompositeGraphSym
09:41:24.592 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 0.002 secs
09:43:37.012 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded TAIR10 mRNA in 0.002 secs