INFO [2017-09-26 22:47:45,779] [Main.java:154]  Startup  IGV Version 2.4.1 09/25/2017 11:46 AM
INFO [2017-09-26 22:47:45,780] [Main.java:155]  Java 1.8.0_31
INFO [2017-09-26 22:47:45,780] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-09-26 22:47:45,997] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-09-26 22:47:45,997] [Main.java:157]  OS: Mac OS X
INFO [2017-09-26 22:47:59,883] [GenomeManager.java:190]  Loading genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome
INFO [2017-09-26 22:48:06,098] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 22:48:06,112] [GenomeManager.java:270]  Genome loaded.  id= hg19
INFO [2017-09-26 22:48:06,285] [CommandListener.java:120]  Listening on port 60151
INFO [2017-09-26 22:49:27,410] [IGV.java:1380]  Loading 1 resources.
INFO [2017-09-26 22:49:27,412] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Downloads/MTB_merged.bam.tdf
INFO [2017-09-26 22:50:05,587] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-09-26 22:50:05,593] [FastaUtils.java:66]  Creating index file at /Users/kpatrick/Downloads/MTB_merged.bam.bai.fai
ERROR [2017-09-26 22:50:05,608] [MessageUtils.java:64]  Could not create index file: /Users/kpatrick/Downloads/MTB_merged.bam.bai.fai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    /Users/kpatrick/Downloads/MTB_merged.bam.bai<br>Blank line at line number 255, followed by data line at 256, in contig null
Blank lines are only allowed at the end of a contig
	at org.broad.igv.feature.genome.fasta.FastaUtils.createIndexFile(FastaUtils.java:144)
	at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:367)
	at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:234)
	at org.broad.igv.ui.IGVMenuBar$10.actionPerformed(IGVMenuBar.java:540)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
	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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:125)
	at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
	at java.awt.MenuItem.processEvent(MenuItem.java:628)
	at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:351)
	at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:339)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:754)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:702)
	at java.awt.EventQueue$3.run(EventQueue.java:696)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:724)
	at java.awt.EventQueue$4.run(EventQueue.java:722)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
	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 [2017-09-26 22:50:05,613] [MessageUtils.java:74]  Could not create index file: /Users/kpatrick/Downloads/MTB_merged.bam.bai.fai
INFO [2017-09-26 22:50:08,173] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 22:50:08,173] [GenomeManager.java:270]  Genome loaded.  id= /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-09-26 22:51:54,703] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 22:52:07,246] [IGV.java:1380]  Loading 1 resources.
INFO [2017-09-26 22:52:07,247] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-09-26 22:52:07,248] [MessageUtils.java:74]  <html><b>ERROR:</b> Loading SAM/BAM index files are not supported:  /Users/kpatrick/Downloads/MTB_merged.bam.bai<br>Load the SAM or BAM file directly. 
INFO [2017-09-26 22:52:26,543] [IGV.java:1380]  Loading 1 resources.
INFO [2017-09-26 22:52:26,544] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Downloads/MTB_merged.bam.crdownload
INFO [2017-09-26 22:52:29,859] [MessageUtils.java:74]  <html>Unknown file type: /Users/kpatrick/Downloads/MTB_merged.bam.crdownload<br>Check file extension
INFO [2017-09-26 22:52:34,332] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 22:52:35,419] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 22:52:35,419] [GenomeComboBox.java:85]  Loading Human hg19
INFO [2017-09-26 22:52:35,421] [GenomeComboBox.java:96]  Loading hg19
INFO [2017-09-26 22:52:35,484] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/hg19.genome
INFO [2017-09-26 22:52:37,913] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 22:52:37,923] [GenomeManager.java:270]  Genome loaded.  id= hg19
INFO [2017-09-26 23:21:09,529] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 23:21:09,531] [GenomeComboBox.java:85]  Loading More...
INFO [2017-09-26 23:21:09,531] [GenomeComboBox.java:96]  Loading More...
INFO [2017-09-26 23:21:23,329] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 23:21:23,329] [GenomeManager.java:190]  Loading genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/mm10.genome
INFO [2017-09-26 23:21:25,564] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 23:21:25,570] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-09-26 23:21:31,458] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 23:21:31,458] [GenomeComboBox.java:85]  Loading MTB_merged.bam.bai
INFO [2017-09-26 23:21:31,459] [GenomeComboBox.java:96]  Loading /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-09-26 23:21:31,514] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-09-26 23:21:31,617] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 23:21:32,062] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-26 23:21:32,067] [GenomeManager.java:270]  Genome loaded.  id= /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-09-26 23:21:40,523] [MessageUtils.java:74]  Cannot find feature or locus: stat1
INFO [2017-09-26 23:21:45,682] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-27 11:46:25,912] [IGV.java:1380]  Loading 1 resources.
INFO [2017-09-27 11:46:25,926] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Downloads/MTB_merged.bam.tdf
ERROR [2017-09-27 11:46:25,989] [TrackLoader.java:271]  
java.lang.NullPointerException
	at org.broad.igv.track.DataSourceTrack.<init>(DataSourceTrack.java:97)
	at org.broad.igv.track.TrackLoader.loadTDFFile(TrackLoader.java:756)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:193)
	at org.broad.igv.ui.IGV.load(IGV.java:1463)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1395)
	at org.broad.igv.ui.IGV$4.run(IGV.java:493)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2017-09-27 11:46:25,992] [IGV.java:1398]  Error loading track
java.lang.NullPointerException
	at org.broad.igv.exceptions.DataLoadException.<init>(DataLoadException.java:38)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:273)
	at org.broad.igv.ui.IGV.load(IGV.java:1463)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1395)
	at org.broad.igv.ui.IGV$4.run(IGV.java:493)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
INFO [2017-09-27 11:46:25,997] [MessageUtils.java:74]  Error loading /Users/kpatrick/Downloads/MTB_merged.bam.tdf: null
INFO [2017-09-27 11:46:58,460] [IGV.java:1380]  Loading 1 resources.
INFO [2017-09-27 11:46:58,461] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Downloads/MTB_merged.bam
INFO [2017-09-27 11:46:58,668] [MessageUtils.java:74]  <html>File: /Users/kpatrick/Downloads/MTB_merged.bam<br>does not contain any sequence names which match the current genome.<br><br>File: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;chr1, chr2, chr3, chr4,  ...<br>Genome: 
INFO [2017-09-27 11:47:06,239] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-27 11:47:06,240] [GenomeComboBox.java:85]  Loading Mouse (mm10)
INFO [2017-09-27 11:47:06,241] [GenomeComboBox.java:96]  Loading mm10
INFO [2017-09-27 11:47:06,291] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-09-27 11:47:08,903] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-09-27 11:47:08,924] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-09-27 11:47:18,776] [IGV.java:1380]  Loading 1 resources.
INFO [2017-09-27 11:47:18,778] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Downloads/MTB_merged.bam
INFO [2017-09-27 11:47:42,129] [HttpUtils.java:851]  Range-byte request succeeded
INFO [2017-09-27 11:51:34,785] [ShutdownThread.java:47]  Shutting down
INFO [2017-10-13 13:11:36,210] [Main.java:154]  Startup  IGV Version 2.4.1 09/25/2017 11:46 AM
INFO [2017-10-13 13:11:36,211] [Main.java:155]  Java 1.8.0_31
INFO [2017-10-13 13:11:36,212] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-10-13 13:11:36,505] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-10-13 13:11:36,505] [Main.java:157]  OS: Mac OS X
INFO [2017-10-13 13:11:48,162] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-10-13 13:11:50,641] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-10-13 13:11:50,651] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-10-13 13:11:50,768] [CommandListener.java:120]  Listening on port 60151
INFO [2017-10-13 13:11:57,711] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-10-13 13:11:57,712] [GenomeComboBox.java:85]  Loading MTB_merged.bam.bai
INFO [2017-10-13 13:11:57,714] [GenomeComboBox.java:96]  Loading /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-10-13 13:11:57,797] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-10-13 13:11:57,963] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-10-13 13:11:58,676] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-10-13 13:11:58,679] [GenomeManager.java:270]  Genome loaded.  id= /Users/kpatrick/Downloads/MTB_merged.bam.bai
INFO [2017-10-13 13:12:05,455] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-10-13 13:12:05,456] [GenomeComboBox.java:85]  Loading Mouse (mm10)
INFO [2017-10-13 13:12:05,456] [GenomeComboBox.java:96]  Loading mm10
INFO [2017-10-13 13:12:05,517] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-10-13 13:12:07,202] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-10-13 13:12:07,226] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-10-13 13:12:34,475] [IGV.java:1380]  Loading 1 resources.
INFO [2017-10-13 13:12:34,480] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Downloads/MTB_merged.bam
INFO [2017-10-13 13:12:52,320] [HttpUtils.java:851]  Range-byte request succeeded
INFO [2017-10-23 14:42:47,074] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-25 12:55:59,534] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-25 12:55:59,535] [Main.java:155]  Java 1.8.0_31
INFO [2017-11-25 12:55:59,535] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-25 12:55:59,808] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-25 12:55:59,809] [Main.java:157]  OS: Mac OS X
INFO [2017-11-25 12:56:12,386] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-25 12:56:14,875] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-25 12:56:14,884] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-25 12:56:15,010] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-25 12:57:04,317] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-27 12:55:23,786] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-27 12:55:23,787] [Main.java:155]  Java 1.8.0_31
INFO [2017-11-27 12:55:23,788] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-27 12:55:24,056] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-27 12:55:24,056] [Main.java:157]  OS: Mac OS X
INFO [2017-11-27 12:55:38,254] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-27 12:55:43,383] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-27 12:55:43,393] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-27 12:55:43,534] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-27 13:03:23,737] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/mm10.genome
ERROR [2017-11-27 13:03:25,530] [MessageUtils.java:64]  /Users/kpatrick/Watson_mouse_IGV_files/ref/GRCm38.primary_assembly.genome.fa.fai (No such file or directory)
java.io.FileNotFoundException: /Users/kpatrick/Watson_mouse_IGV_files/ref/GRCm38.primary_assembly.genome.fa.fai (No such file or directory)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:118)
	at org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:96)
	at org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:78)
	at org.broad.igv.feature.genome.fasta.FastaIndex.parseIndexFile(FastaIndex.java:89)
	at org.broad.igv.feature.genome.fasta.FastaIndex.<init>(FastaIndex.java:55)
	at org.broad.igv.feature.genome.fasta.FastaIndexedSequence.<init>(FastaIndexedSequence.java:65)
	at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:471)
	at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:210)
	at org.broad.igv.ui.IGVMenuBar$10.actionPerformed(IGVMenuBar.java:540)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
	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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:125)
	at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
	at java.awt.MenuItem.processEvent(MenuItem.java:628)
	at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:351)
	at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:339)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:754)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:702)
	at java.awt.EventQueue$3.run(EventQueue.java:696)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:724)
	at java.awt.EventQueue$4.run(EventQueue.java:722)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
	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 [2017-11-27 13:03:25,532] [MessageUtils.java:74]  /Users/kpatrick/Watson_mouse_IGV_files/ref/GRCm38.primary_assembly.genome.fa.fai (No such file or directory)
INFO [2017-11-27 21:15:50,683] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/mm10.genome
ERROR [2017-11-27 21:15:52,345] [MessageUtils.java:64]  /Users/kpatrick/Watson_mouse_IGV_files/ref/GRCm38.primary_assembly.genome.fa.fai (No such file or directory)
java.io.FileNotFoundException: /Users/kpatrick/Watson_mouse_IGV_files/ref/GRCm38.primary_assembly.genome.fa.fai (No such file or directory)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:118)
	at org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:96)
	at org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:78)
	at org.broad.igv.feature.genome.fasta.FastaIndex.parseIndexFile(FastaIndex.java:89)
	at org.broad.igv.feature.genome.fasta.FastaIndex.<init>(FastaIndex.java:55)
	at org.broad.igv.feature.genome.fasta.FastaIndexedSequence.<init>(FastaIndexedSequence.java:65)
	at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:471)
	at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:210)
	at org.broad.igv.ui.IGVMenuBar$10.actionPerformed(IGVMenuBar.java:540)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
	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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:125)
	at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
	at java.awt.MenuItem.processEvent(MenuItem.java:628)
	at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:351)
	at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:339)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:754)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:702)
	at java.awt.EventQueue$3.run(EventQueue.java:696)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:724)
	at java.awt.EventQueue$4.run(EventQueue.java:722)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
	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 [2017-11-27 21:15:52,346] [MessageUtils.java:74]  /Users/kpatrick/Watson_mouse_IGV_files/ref/GRCm38.primary_assembly.genome.fa.fai (No such file or directory)
INFO [2017-11-29 12:41:47,556] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/GRCm38.primary_assembly.genome.fa.gz
ERROR [2017-11-29 12:41:47,567] [MessageUtils.java:64]  IGV cannot readed gzipped fasta files.
org.broad.igv.feature.genome.GenomeException: IGV cannot readed gzipped fasta files.
	at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:225)
	at org.broad.igv.ui.IGVMenuBar$10.actionPerformed(IGVMenuBar.java:540)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
	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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:125)
	at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
	at java.awt.MenuItem.processEvent(MenuItem.java:628)
	at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:351)
	at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:339)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:754)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:702)
	at java.awt.EventQueue$3.run(EventQueue.java:696)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:724)
	at java.awt.EventQueue$4.run(EventQueue.java:722)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
	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 [2017-11-29 12:41:47,570] [MessageUtils.java:74]  IGV cannot readed gzipped fasta files.
INFO [2017-11-29 12:42:34,534] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/GRCm38.primary_assembly.genome.fa
INFO [2017-11-29 12:42:36,171] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 12:42:36,173] [GenomeManager.java:270]  Genome loaded.  id= /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/GRCm38.primary_assembly.genome.fa
INFO [2017-11-29 12:42:48,892] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-29 12:42:48,892] [Main.java:155]  Java 1.8.0_31
INFO [2017-11-29 12:42:48,892] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-29 12:42:49,130] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-29 12:42:49,131] [Main.java:157]  OS: Mac OS X
INFO [2017-11-29 12:43:01,568] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/GRCm38.primary_assembly.genome.fa
INFO [2017-11-29 12:43:01,608] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 12:43:02,601] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 12:43:02,615] [GenomeManager.java:270]  Genome loaded.  id= /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/GRCm38.primary_assembly.genome.fa
INFO [2017-11-29 12:43:02,777] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-29 12:43:07,435] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 12:43:11,313] [MessageUtils.java:74]  Cannot find feature or locus: stat1
INFO [2017-11-29 12:58:13,749] [MessageUtils.java:74]  <html>Descriptive name is required
INFO [2017-11-29 12:58:36,357] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 12:58:36,357] [IGVCommandBar.java:165]  Selecting genome Mouse genome
INFO [2017-11-29 12:58:36,360] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 12:58:36,361] [GenomeComboBox.java:85]  Loading Mouse genome
INFO [2017-11-29 12:58:36,362] [GenomeComboBox.java:96]  Loading Mouse genome
INFO [2017-11-29 12:58:36,465] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/Mouse genome.genome
INFO [2017-11-29 13:22:47,063] [MessageUtils.java:74]  Cannot find feature or locus: stat1
INFO [2017-11-29 13:22:49,169] [MessageUtils.java:74]  Cannot find feature or locus: stat1
INFO [2017-11-29 13:22:59,186] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 13:23:02,546] [MessageUtils.java:74]  Cannot find feature or locus: stat1
INFO [2017-11-29 13:23:07,485] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 13:23:07,486] [GenomeComboBox.java:85]  Loading Mouse (mm10)
INFO [2017-11-29 13:23:07,487] [GenomeComboBox.java:96]  Loading mm10
INFO [2017-11-29 13:23:07,553] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-29 13:23:10,889] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-29 13:23:10,903] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-29 22:03:09,102] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-29 22:03:09,121] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
ERROR [2017-11-29 22:03:13,347] [AlignmentReaderFactory.java:90]  Index file not found.  Tried <br>/Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bai
org.broad.igv.exceptions.DataLoadException: Index file not found.  Tried <br>/Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bai
	at org.broad.igv.sam.reader.BAMReader.getIndexPath(BAMReader.java:300)
	at org.broad.igv.sam.reader.BAMReader.getSamReader(BAMReader.java:104)
	at org.broad.igv.sam.reader.BAMReader.<init>(BAMReader.java:67)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:88)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:60)
	at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:75)
	at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:930)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:176)
	at org.broad.igv.ui.IGV.load(IGV.java:1463)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1395)
	at org.broad.igv.ui.IGV$4.run(IGV.java:493)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2017-11-29 22:03:13,353] [TrackLoader.java:271]  An error occurred while accessing:    /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam<br>Error loading BAM file: org.broad.igv.exceptions.DataLoadException: Index file not found.  Tried <br>/Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam<br>Error loading BAM file: org.broad.igv.exceptions.DataLoadException: Index file not found.  Tried <br>/Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bai
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:91)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:60)
	at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:75)
	at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:930)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:176)
	at org.broad.igv.ui.IGV.load(IGV.java:1463)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1395)
	at org.broad.igv.ui.IGV$4.run(IGV.java:493)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2017-11-29 22:03:13,354] [IGV.java:1398]  Error loading track
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam<br>Error loading BAM file: org.broad.igv.exceptions.DataLoadException: Index file not found.  Tried <br>/Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bai
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:273)
	at org.broad.igv.ui.IGV.load(IGV.java:1463)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1395)
	at org.broad.igv.ui.IGV$4.run(IGV.java:493)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
INFO [2017-11-29 22:03:13,355] [MessageUtils.java:74]  Error loading /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam: An error occurred while accessing:    /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam<br>Error loading BAM file: org.broad.igv.exceptions.DataLoadException: Index file not found.  Tried <br>/Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bai
INFO [2017-11-30 09:13:24,861] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:13:24,868] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 09:13:38,672] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 09:14:23,275] [MessageUtils.java:74]  Cannot find feature or locus: iptr1
INFO [2017-11-30 09:14:33,963] [MessageUtils.java:74]  Cannot find feature or locus: iptr1
INFO [2017-11-30 09:16:45,680] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:16:45,681] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.primary_assembly.annotation.sorted.gtf
INFO [2017-11-30 09:17:21,451] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:17:21,451] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.UCSC_canonical_subset.annotation.sorted.gtf
INFO [2017-11-30 09:25:22,310] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:25:22,315] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 09:44:23,909] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 09:47:46,710] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 09:47:46,711] [Main.java:155]  Java 1.8.0_31
INFO [2017-11-30 09:47:46,711] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 09:47:47,011] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 09:47:47,011] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 09:48:01,657] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 09:48:05,390] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 09:48:05,413] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 09:48:05,584] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 09:48:48,998] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:48:49,001] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 09:53:53,794] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:53:53,799] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
ERROR [2017-11-30 09:54:30,059] [IGVSessionReader.java:312]  Load session error
com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
	at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.invalidByte(UTF8Reader.java:691)
	at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.read(UTF8Reader.java:557)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1743)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.arrangeCapacity(XMLEntityScanner.java:1614)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.skipString(XMLEntityScanner.java:1652)
	at com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:196)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:812)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:348)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1158)
	at org.broad.igv.ui.IGV$8.run(IGV.java:1127)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2017-11-30 09:54:30,071] [IGV.java:1192]  Error loading session session : <br>&nbsp;&nbsp;/Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam<br>com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
java.lang.RuntimeException: com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:313)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1158)
	at org.broad.igv.ui.IGV$8.run(IGV.java:1127)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
	at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.invalidByte(UTF8Reader.java:691)
	at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.read(UTF8Reader.java:557)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1743)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.arrangeCapacity(XMLEntityScanner.java:1614)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.skipString(XMLEntityScanner.java:1652)
	at com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:196)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:812)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:348)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	... 7 more
INFO [2017-11-30 09:54:30,086] [MessageUtils.java:74]  <html>Unexpected error: java.lang.RuntimeException: com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence..<br>See igv.log for more details
ERROR [2017-11-30 09:54:30,087] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.RuntimeException: com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1193)
	at org.broad.igv.ui.IGV$8.run(IGV.java:1127)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:313)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1158)
	... 6 more
Caused by: com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
	at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.invalidByte(UTF8Reader.java:691)
	at com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.read(UTF8Reader.java:557)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1743)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.arrangeCapacity(XMLEntityScanner.java:1614)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.skipString(XMLEntityScanner.java:1652)
	at com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:196)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:812)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:348)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	... 7 more
INFO [2017-11-30 09:54:39,452] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:54:39,454] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 09:54:46,525] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:54:46,526] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 09:54:52,351] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 09:56:28,834] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 09:56:28,836] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 10:05:47,060] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 10:05:47,061] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 10:13:14,865] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 10:17:19,330] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 10:17:19,330] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 10:17:19,331] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 10:17:19,555] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 10:17:19,556] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 10:17:38,308] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 10:17:41,331] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 10:17:41,340] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 10:17:41,477] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 10:18:00,853] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 10:18:00,859] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 10:18:28,406] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 10:19:32,696] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 10:19:32,697] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 10:19:41,736] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 10:19:41,736] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 10:41:34,948] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 10:41:34,956] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 10:41:34,978] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 10:41:35,129] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 10:43:38,829] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 10:43:38,834] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 10:43:58,476] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 10:43:58,477] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 10:43:58,477] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 10:43:58,598] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 10:43:58,599] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 10:44:11,588] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 10:44:14,382] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 10:44:14,392] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 10:44:14,597] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 10:45:21,963] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 10:45:21,965] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 10:45:22,244] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 10:45:22,343] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 10:47:21,525] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 10:55:08,223] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 10:55:08,229] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 10:56:44,544] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 10:56:44,544] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 10:56:44,544] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 10:56:44,668] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 10:56:44,668] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 10:56:57,258] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 10:57:00,367] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 10:57:00,377] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 10:57:00,508] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 10:59:11,867] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 10:59:11,870] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 10:59:12,140] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 10:59:12,211] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 11:02:00,815] [HttpUtils.java:864]  Range-byte request succeeded
ERROR [2017-11-30 11:16:27,057] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at org.broad.igv.sam.AlignmentPacker.packAlignments(AlignmentPacker.java:73)
	at org.broad.igv.sam.AlignmentInterval.packAlignments(AlignmentInterval.java:170)
	at org.broad.igv.sam.AlignmentDataManager.packAlignments(AlignmentDataManager.java:257)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:312)
	at org.broad.igv.sam.SpliceJunctionTrack.load(SpliceJunctionTrack.java:266)
	at org.broad.igv.ui.SashimiPlot.<init>(SashimiPlot.java:140)
	at org.broad.igv.ui.SashimiPlot.getSashimiPlot(SashimiPlot.java:654)
	at org.broad.igv.sam.SpliceJunctionTrack$1.actionPerformed(SpliceJunctionTrack.java:173)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$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 [2017-11-30 11:27:51,162] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 11:28:55,004] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 11:28:55,004] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 11:28:55,004] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 11:28:55,139] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 11:28:55,139] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 11:29:07,710] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 11:29:10,533] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 11:29:10,544] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 11:29:10,696] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 11:29:31,606] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 11:29:31,607] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 11:29:31,948] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 11:29:32,026] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 11:29:43,978] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 11:32:10,770] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 11:32:28,413] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 11:32:28,414] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 11:32:28,414] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 11:32:28,556] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 11:32:28,556] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 11:32:39,741] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 11:32:42,914] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 11:32:42,923] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 11:32:43,060] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 11:33:13,022] [IGV.java:1380]  Loading 2 resources.
INFO [2017-11-30 11:33:13,027] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 11:33:13,535] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 11:33:21,747] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 11:36:55,970] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 11:37:17,599] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 11:37:17,599] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 11:37:17,599] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 11:37:17,722] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 11:37:17,723] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 11:37:28,675] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 11:37:31,645] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 11:37:31,660] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 11:37:31,810] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 11:37:50,140] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 11:37:50,141] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 11:37:50,447] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 11:37:50,525] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 11:39:40,162] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 11:40:13,096] [MessageUtils.java:74]  Cannot find feature or locus: igrm2
INFO [2017-11-30 12:02:14,456] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 12:02:14,460] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.primary_assembly.annotation.sorted.gtf
INFO [2017-11-30 12:03:05,372] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 12:03:05,373] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.UCSC_canonical_subset.annotation.sorted.gtf
INFO [2017-11-30 12:45:31,042] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 12:45:31,049] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.primary_assembly.conanical.annotation.sorted.gtf
INFO [2017-11-30 13:02:31,443] [MessageUtils.java:74]  Cannot find feature or locus: chr10:42,Cxcl10500,054-42,537,369
INFO [2017-11-30 13:08:43,520] [MessageUtils.java:74]  Cannot find feature or locus: chr5:1myd8842,901,115-142,908,754
INFO [2017-11-30 14:48:46,894] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 14:48:46,905] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 15:00:31,818] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 15:00:31,822] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 15:00:31,822] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 15:00:31,929] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 15:00:31,929] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 15:00:44,342] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 15:00:46,421] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 15:00:46,430] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 15:00:46,568] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 15:01:14,771] [IGV.java:1380]  Loading 6 resources.
INFO [2017-11-30 15:01:14,774] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 15:01:15,011] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 15:01:15,093] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 15:01:15,244] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.UCSC_canonical_subset.annotation.sorted.gtf
INFO [2017-11-30 15:01:15,527] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.primary_assembly.annotation.sorted.gtf
INFO [2017-11-30 15:01:15,629] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/gencode.vM15.primary_assembly.conanical.annotation.sorted.gtf
INFO [2017-11-30 15:01:26,143] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 15:03:11,626] [MessageUtils.java:74]  Cannot find feature or locus: trim19
INFO [2017-11-30 15:06:50,947] [MessageUtils.java:74]  Cannot find feature or locus: phf15
INFO [2017-11-30 15:17:53,915] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 15:18:25,084] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 15:18:25,084] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 15:18:25,084] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 15:18:25,285] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 15:18:25,285] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 15:18:38,034] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 15:18:41,636] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 15:18:41,651] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 15:18:41,858] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 15:53:58,067] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 15:53:58,082] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 15:53:58,581] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 15:53:58,670] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 15:54:27,472] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 15:55:23,809] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 15:56:38,154] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 15:56:38,155] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 15:56:38,155] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 15:56:38,249] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 15:56:38,249] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 15:56:51,846] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 15:56:55,244] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 15:56:55,254] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 15:56:55,407] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 15:57:10,759] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 15:57:10,763] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 15:57:11,116] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 15:57:11,227] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 15:57:15,623] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 16:03:03,255] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 16:03:03,258] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:03:03,303] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:03:03,342] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:03:30,028] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:03:35,498] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:03:35,499] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:03:35,499] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:03:35,626] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:03:35,626] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:03:48,524] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:03:51,962] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:03:51,974] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:03:52,151] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 16:04:31,689] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:04:31,694] [FastaUtils.java:66]  Creating index file at /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam.fai
ERROR [2017-11-30 16:04:31,709] [MessageUtils.java:64]  Could not create index file: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam.fai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam<br>Blank line at line number 181, followed by data line at 182, in contig null
Blank lines are only allowed at the end of a contig
	at org.broad.igv.feature.genome.fasta.FastaUtils.createIndexFile(FastaUtils.java:144)
	at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:367)
	at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:234)
	at org.broad.igv.ui.IGVMenuBar$10.actionPerformed(IGVMenuBar.java:540)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:125)
	at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
	at java.awt.MenuItem.processEvent(MenuItem.java:628)
	at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:357)
	at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:345)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:761)
	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 [2017-11-30 16:04:31,711] [MessageUtils.java:74]  Could not create index file: /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam.fai
INFO [2017-11-30 16:04:34,956] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:04:34,957] [GenomeManager.java:270]  Genome loaded.  id= /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:04:43,198] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:04:43,199] [GenomeComboBox.java:85]  Loading Mouse (mm10)
INFO [2017-11-30 16:04:43,201] [GenomeComboBox.java:96]  Loading mm10
INFO [2017-11-30 16:04:43,271] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:04:45,292] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:04:45,320] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:04:53,784] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 16:04:53,788] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:04:54,015] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:04:54,079] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:05:05,225] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 16:06:25,824] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:10:14,379] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:10:14,380] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:10:14,381] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:10:14,560] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:10:14,561] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:10:26,086] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:10:28,908] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:10:28,919] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:10:29,045] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 16:10:34,937] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:10:38,186] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:10:43,233] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:10:43,233] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:10:43,233] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:10:43,326] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:10:43,326] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:10:54,756] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:10:59,355] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:10:59,373] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:11:00,001] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 16:11:02,498] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:11:24,161] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:11:24,162] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:11:24,165] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:11:24,339] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:11:24,340] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:11:36,550] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:11:39,088] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:11:39,095] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:11:39,221] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 16:11:50,569] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 16:11:50,571] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:11:50,906] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:11:50,995] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:12:05,624] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 16:19:59,779] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:23:10,298] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:23:10,298] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:23:10,299] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:23:10,307] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:23:10,308] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:23:12,280] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:23:15,824] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:23:15,848] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:23:15,909] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 16:25:36,470] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 16:25:36,474] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:25:36,845] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:25:36,998] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:25:49,859] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:25:56,728] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:25:56,728] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:25:56,728] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:25:56,847] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:25:56,848] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:26:02,912] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:26:15,099] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:26:15,099] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:26:15,100] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:26:15,104] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:26:15,104] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:26:16,417] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:26:19,504] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:26:19,514] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:26:19,581] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 16:26:33,915] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 16:26:33,917] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:26:34,175] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:26:34,277] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:27:06,398] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 16:27:58,448] [ShutdownThread.java:47]  Shutting down
INFO [2017-11-30 16:30:28,417] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-11-30 16:30:28,418] [Main.java:155]  Java 1.8.0_151
INFO [2017-11-30 16:30:28,419] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-11-30 16:30:28,435] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-11-30 16:30:28,436] [Main.java:157]  OS: Mac OS X
INFO [2017-11-30 16:30:29,878] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-11-30 16:30:33,485] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-11-30 16:30:33,505] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-11-30 16:30:33,572] [CommandListener.java:120]  Listening on port 60151
INFO [2017-11-30 16:30:49,050] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 16:30:49,053] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:30:49,326] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:30:49,423] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:31:11,564] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-11-30 16:37:42,422] [MessageUtils.java:74]  Cannot find feature or locus: ifi213
INFO [2017-11-30 16:51:40,511] [IGV.java:1380]  Loading 3 resources.
INFO [2017-11-30 16:51:40,512] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:51:40,584] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:51:40,677] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:52:28,436] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 16:52:28,437] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-11-30 16:52:51,420] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 16:52:51,420] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-11-30 16:53:16,744] [IGV.java:1380]  Loading 1 resources.
INFO [2017-11-30 16:53:16,744] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-11-30 16:54:53,585] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 09:39:40,244] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 09:39:40,244] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 09:39:40,244] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 09:39:40,251] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 09:39:40,251] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 09:39:41,524] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 09:39:45,119] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 09:39:45,142] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 09:39:45,216] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 09:42:26,238] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 09:42:26,240] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 09:42:32,322] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 09:42:32,323] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-01 09:42:37,764] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 09:42:37,764] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 09:42:42,825] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 11:10:30,148] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 11:10:48,898] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 11:10:48,898] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 11:10:48,898] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 11:10:48,903] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 11:10:48,903] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 11:10:49,808] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 11:10:52,857] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 11:10:52,867] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 11:10:52,913] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 11:14:55,745] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 11:14:55,747] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 11:14:59,879] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 11:14:59,880] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-01 11:15:04,802] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 11:15:04,802] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 11:15:08,575] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 11:44:59,076] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 13:26:05,909] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 13:26:05,909] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 13:26:05,909] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 13:26:05,913] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 13:26:05,914] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 13:26:07,351] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 13:26:10,142] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 13:26:10,151] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 13:26:10,213] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 13:26:29,236] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 13:26:29,237] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 13:26:36,431] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 13:26:36,432] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-01 13:26:41,438] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 13:26:41,439] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 13:32:00,826] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 13:36:21,094] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 14:01:18,470] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 14:01:18,471] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 14:01:18,471] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 14:01:18,477] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 14:01:18,477] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 14:01:19,780] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 14:01:22,174] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 14:01:22,183] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 14:01:22,221] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 14:01:30,208] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:01:30,210] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 14:01:35,773] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:01:35,774] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-01 14:01:43,413] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:01:43,414] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 14:02:05,219] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 14:02:39,839] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 14:02:53,891] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 14:02:53,891] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 14:02:53,891] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 14:02:53,896] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 14:02:53,896] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 14:02:54,893] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 14:02:57,614] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 14:02:57,622] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 14:02:57,660] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 14:03:07,811] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:03:07,812] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 14:03:19,306] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:03:19,307] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 14:03:52,195] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 14:45:11,443] [MessageUtils.java:74]  Cannot find feature or locus: trim30c
INFO [2017-12-01 14:46:38,475] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 14:46:49,513] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 14:46:49,514] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 14:46:49,514] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 14:46:49,519] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 14:46:49,519] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 14:46:50,855] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 14:46:54,108] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 14:46:54,120] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 14:46:54,171] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 14:55:28,067] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:55:28,068] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 14:55:34,228] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:55:34,229] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-01 14:55:41,630] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 14:55:41,630] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 14:55:51,507] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 14:58:14,292] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 15:02:43,639] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 15:02:43,639] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 15:02:43,639] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 15:02:43,643] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 15:02:43,643] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 15:02:44,509] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 15:02:46,986] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 15:02:46,995] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 15:02:47,031] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 15:02:56,964] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 15:02:56,965] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 15:03:05,445] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 15:03:05,446] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 15:03:13,239] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 15:07:09,761] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 15:09:23,092] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 15:09:23,095] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 15:09:23,095] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 15:09:23,100] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 15:09:23,100] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 15:09:23,987] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 15:09:26,251] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 15:09:26,261] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 15:09:26,309] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 15:09:58,858] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 15:09:58,859] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 15:10:20,763] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 15:10:20,764] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-01 15:10:26,245] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 15:10:26,246] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 15:10:36,892] [HttpUtils.java:864]  Range-byte request succeeded
WARN [2017-12-01 15:27:16,030] [SequenceWrapper.java:241]  Null sequence for chr11:116000000-117000000
INFO [2017-12-01 15:48:34,321] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 16:03:49,415] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 16:03:49,416] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 16:03:49,416] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 16:03:49,421] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 16:03:49,421] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 16:03:50,844] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 16:03:53,563] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 16:03:53,571] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 16:03:53,607] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 16:04:14,011] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 16:04:14,012] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 16:04:14,547] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 16:04:18,455] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 16:04:18,456] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-01 16:04:24,427] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 16:04:24,427] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-01 16:21:32,980] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 16:21:32,983] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 16:23:35,366] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 16:23:35,366] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 16:23:35,367] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 16:23:35,370] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 16:23:35,370] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 16:23:36,488] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 16:23:39,143] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 16:23:39,153] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 16:23:39,188] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 16:24:27,581] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 16:24:27,582] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 16:24:34,390] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 16:36:25,746] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 16:39:43,058] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 16:39:43,059] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 16:39:43,059] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 16:39:43,065] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 16:39:43,065] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 16:39:43,934] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 16:39:46,407] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 16:39:46,414] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 16:39:46,452] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 16:39:57,829] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 16:39:57,830] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 16:40:18,214] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-01 16:40:40,549] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-01 16:40:55,457] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-01 16:40:55,458] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-01 16:40:55,458] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-01 16:40:55,462] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-01 16:40:55,463] [Main.java:157]  OS: Mac OS X
INFO [2017-12-01 16:40:56,486] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-01 16:40:59,303] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-01 16:40:59,311] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-01 16:40:59,344] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-01 16:41:11,223] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-01 16:41:11,225] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-01 16:41:25,499] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 09:35:52,165] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 09:36:07,173] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 09:36:07,173] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 09:36:07,173] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 09:36:07,182] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 09:36:07,183] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 09:36:09,669] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 09:36:11,707] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 09:36:11,717] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 09:36:11,752] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 09:36:32,304] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 09:36:32,305] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 09:36:37,646] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 09:36:37,646] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 09:36:42,054] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 09:36:42,055] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 09:37:06,877] [HttpUtils.java:864]  Range-byte request succeeded
ERROR [2017-12-04 09:37:09,894] [AlignmentTileLoader.java:300]  Error loading alignment data
java.util.ConcurrentModificationException
	at java.util.ArrayList.sort(ArrayList.java:1462)
	at org.broad.igv.sam.InsertionManager.processAlignments(InsertionManager.java:146)
	at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:287)
	at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:334)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:309)
	at org.broad.igv.sam.CoverageTrack.load(CoverageTrack.java:187)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:226)
	at java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1626)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
INFO [2017-12-04 09:37:09,894] [MessageUtils.java:74]  <html>Error encountered querying alignments: java.util.ConcurrentModificationException
INFO [2017-12-04 09:55:20,245] [ShutdownThread.java:47]  Shutting down
ERROR [2017-12-04 09:55:20,247] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.IllegalStateException: zip file closed
	at java.util.zip.ZipFile.ensureOpen(ZipFile.java:686)
	at java.util.zip.ZipFile.getEntry(ZipFile.java:315)
	at java.util.jar.JarFile.getEntry(JarFile.java:240)
	at com.sun.deploy.cache.CachedJarFile.getEntry(Unknown Source)
	at java.util.jar.JarFile.getJarEntry(JarFile.java:223)
	at com.sun.deploy.security.DeployURLClassPath$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:357)
	at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:48)
	at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:60)
INFO [2017-12-04 09:55:31,457] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 09:55:31,458] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 09:55:31,458] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 09:55:31,468] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 09:55:31,469] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 09:55:32,939] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 09:55:35,230] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 09:55:35,240] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 09:55:35,274] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 09:56:25,242] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 09:56:25,244] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 09:56:30,055] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 09:56:30,055] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 09:56:33,945] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 09:56:33,946] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 09:56:39,008] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 10:09:23,717] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 10:09:35,544] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 10:09:35,545] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 10:09:35,545] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 10:09:35,550] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 10:09:35,551] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 10:09:36,466] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 10:09:38,859] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 10:09:38,867] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 10:09:38,906] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 10:09:46,704] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:09:46,705] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 10:09:50,448] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:09:50,449] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 10:09:55,080] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:09:55,081] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 10:09:59,533] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 10:14:00,311] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 10:16:08,204] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 10:16:08,205] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 10:16:08,205] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 10:16:08,209] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 10:16:08,209] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 10:16:09,088] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 10:16:11,117] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 10:16:11,126] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 10:16:11,159] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 10:16:26,072] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:16:26,073] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 10:16:30,265] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:16:30,265] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 10:16:34,992] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:16:34,993] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 10:16:59,379] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 10:21:51,722] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 10:22:01,167] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 10:22:01,167] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 10:22:01,167] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 10:22:01,172] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 10:22:01,173] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 10:22:02,057] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 10:22:04,141] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 10:22:04,148] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 10:22:04,189] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 10:22:35,386] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:22:35,387] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 10:22:39,998] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:22:39,998] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 10:22:45,871] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:22:45,871] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 10:22:51,917] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 10:25:39,354] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 10:25:53,249] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 10:25:53,249] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 10:25:53,250] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 10:25:53,253] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 10:25:53,253] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 10:25:54,198] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 10:25:56,677] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 10:25:56,688] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 10:25:56,736] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 10:26:02,544] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:26:02,545] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 10:26:08,562] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:26:08,563] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 10:26:21,626] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 10:29:19,405] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 10:32:59,290] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 10:32:59,291] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 10:32:59,291] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 10:32:59,296] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 10:32:59,296] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 10:33:00,148] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 10:33:01,971] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 10:33:01,980] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 10:33:02,018] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 10:33:09,636] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:33:09,638] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 10:33:15,378] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:33:15,379] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 10:33:22,215] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 10:34:00,016] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 10:38:55,779] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 10:38:55,779] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 10:38:55,779] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 10:38:55,871] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 10:38:55,871] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 10:39:05,782] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 10:39:07,989] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 10:39:07,997] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 10:39:08,126] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 10:39:31,455] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:39:31,458] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 10:39:37,521] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:39:37,522] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 10:39:41,894] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 10:39:41,894] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 10:39:53,066] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 11:36:01,668] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 11:36:08,125] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 11:36:08,125] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 11:36:08,125] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 11:36:08,204] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 11:36:08,205] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 11:36:19,437] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 11:36:24,613] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 11:36:24,622] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 11:36:24,742] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 11:36:34,482] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 11:36:34,483] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 11:36:40,551] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 11:36:40,554] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 11:36:45,758] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 11:36:45,760] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 11:36:50,277] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-04 13:50:15,745] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-04 13:50:22,453] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-04 13:50:22,454] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-04 13:50:22,454] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-04 13:50:22,534] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-04 13:50:22,535] [Main.java:157]  OS: Mac OS X
INFO [2017-12-04 13:50:34,309] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-04 13:50:36,879] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-04 13:50:36,890] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-04 13:50:37,048] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-04 13:50:50,588] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 13:50:50,589] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-04 13:50:55,858] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 13:50:55,858] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-04 13:51:00,850] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-04 13:51:00,851] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-04 13:51:38,063] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-05 10:53:12,389] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-05 10:53:23,324] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-05 10:53:23,324] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-05 10:53:23,324] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-05 10:53:23,502] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-05 10:53:23,502] [Main.java:157]  OS: Mac OS X
INFO [2017-12-05 10:53:37,549] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-05 10:53:40,673] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-05 10:53:40,687] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-05 10:53:40,854] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-05 10:53:48,626] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-05 10:53:48,629] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-05 10:53:54,256] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-05 10:53:54,256] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-05 10:54:00,387] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-05 10:54:00,389] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-05 10:54:12,161] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 13:36:00,578] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 13:36:00,600] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 13:36:09,724] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 13:36:09,724] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 13:36:09,724] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 13:36:09,952] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 13:36:09,952] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 13:36:25,295] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 13:36:28,172] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 13:36:28,184] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 13:36:28,361] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 13:36:54,767] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 13:36:54,768] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 13:37:01,286] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 13:37:01,287] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 13:37:07,328] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 13:37:07,330] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-06 13:37:22,245] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 13:38:40,470] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 13:38:52,371] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 13:38:52,371] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 13:38:52,371] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 13:38:52,454] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 13:38:52,455] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 13:39:02,781] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 13:39:05,385] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 13:39:05,395] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 13:39:05,534] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 13:39:26,161] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 13:39:26,162] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 13:39:32,993] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 13:39:32,994] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 13:39:55,386] [MessageUtils.java:74]  Cannot find feature or locus: lrmda
INFO [2017-12-06 13:40:11,850] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 13:45:48,800] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 13:47:47,690] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 13:47:47,691] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 13:47:47,692] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 13:47:48,266] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 13:47:48,267] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 13:48:13,268] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 13:48:16,107] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 13:48:16,121] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 13:48:16,285] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 13:48:33,323] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 13:48:33,329] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 13:48:44,227] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 13:48:44,228] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 13:48:57,073] [MessageUtils.java:74]  Cannot find feature or locus: twnk
INFO [2017-12-06 13:49:11,661] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 13:49:54,939] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 13:58:03,658] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 13:58:03,658] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 13:58:03,659] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 13:58:03,873] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 13:58:03,873] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 13:58:19,385] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 13:58:21,650] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 13:58:21,661] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 13:58:21,806] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 13:58:33,699] [IGV.java:1380]  Loading 2 resources.
INFO [2017-12-06 13:58:33,701] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 13:58:33,979] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 13:58:54,416] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 13:59:37,123] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 13:59:43,733] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 13:59:43,733] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 13:59:43,734] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 13:59:43,831] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 13:59:43,831] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 13:59:56,034] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 13:59:59,042] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 13:59:59,053] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 13:59:59,198] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 14:00:42,469] [IGV.java:1380]  Loading 2 resources.
INFO [2017-12-06 14:00:42,470] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 14:00:42,734] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 14:00:54,192] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 14:01:25,596] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 14:10:53,735] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 14:10:53,735] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 14:10:53,736] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 14:10:53,894] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 14:10:53,894] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 14:11:15,771] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 14:11:21,657] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 14:11:21,673] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 14:11:21,806] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 14:13:24,879] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:13:24,881] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 14:13:31,366] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:13:31,367] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 14:13:35,865] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:13:35,866] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-06 14:16:28,854] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 14:23:19,938] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 14:23:31,266] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 14:23:31,267] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 14:23:31,267] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 14:23:31,355] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 14:23:31,356] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 14:23:44,335] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 14:23:47,705] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 14:23:47,721] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 14:23:47,873] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 14:24:42,921] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:24:42,922] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 14:25:08,193] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 14:26:37,567] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:26:37,569] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 14:30:38,420] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 14:30:49,455] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 14:30:49,456] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 14:30:49,456] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 14:30:49,565] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 14:30:49,566] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 14:31:01,629] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 14:31:06,898] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 14:31:06,907] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 14:31:07,061] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 14:31:21,306] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:31:21,307] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 14:31:28,020] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:31:28,021] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 14:32:20,962] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 14:34:17,380] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 14:36:46,687] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 14:36:46,687] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 14:36:46,687] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 14:36:46,772] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 14:36:46,772] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 14:36:57,881] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 14:37:00,421] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 14:37:00,432] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 14:37:00,558] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 14:37:22,990] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:37:22,991] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 14:37:29,389] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:37:29,389] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 14:38:08,908] [HttpUtils.java:864]  Range-byte request succeeded
ERROR [2017-12-06 14:38:44,696] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at org.broad.igv.track.FeatureTrack.setVisibilityWindow(FeatureTrack.java:972)
	at org.broad.igv.track.TrackMenuUtils.changeFeatureVisibilityWindow(TrackMenuUtils.java:1152)
	at org.broad.igv.track.TrackMenuUtils$32.actionPerformed(TrackMenuUtils.java:1473)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$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 [2017-12-06 14:38:58,635] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException
	at org.broad.igv.track.FeatureTrack.setVisibilityWindow(FeatureTrack.java:972)
	at org.broad.igv.track.TrackMenuUtils.changeFeatureVisibilityWindow(TrackMenuUtils.java:1152)
	at org.broad.igv.track.TrackMenuUtils$32.actionPerformed(TrackMenuUtils.java:1473)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$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 [2017-12-06 14:43:43,743] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 14:43:48,736] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 14:43:48,736] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 14:43:48,736] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 14:43:48,833] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 14:43:48,833] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 14:44:00,875] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 14:44:03,675] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 14:44:03,691] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 14:44:03,830] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 14:44:43,641] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:44:43,642] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 14:44:49,387] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:44:49,389] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 14:45:26,093] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 14:49:16,369] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 14:49:16,373] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 14:52:05,055] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 14:52:05,056] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 14:52:05,056] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 14:52:05,061] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 14:52:05,062] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 14:52:06,356] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 14:52:10,739] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 14:52:10,754] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 14:52:10,809] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 14:52:18,232] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:52:18,234] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 14:52:24,272] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:52:24,272] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 14:52:29,645] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 14:52:29,645] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-06 14:53:30,638] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 14:59:06,456] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 15:02:28,385] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 15:02:28,385] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 15:02:28,386] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 15:02:28,389] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 15:02:28,390] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 15:02:29,561] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 15:02:32,173] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 15:02:32,188] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-06 15:02:32,242] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-06 15:02:43,229] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 15:02:43,230] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 15:02:49,402] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 15:02:49,403] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-06 15:02:58,012] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 15:02:58,013] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 15:04:03,692] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 15:26:57,484] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-06 15:26:57,484] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-06 15:26:57,485] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-06 15:26:57,490] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-06 15:26:57,490] [Main.java:157]  OS: Mac OS X
INFO [2017-12-06 15:26:59,048] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-06 15:27:03,972] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-06 15:27:03,996] [GenomeManager.java:270]  Genome loaded.  id= mm10
ERROR [2017-12-06 15:27:04,035] [CommandListener.java:141]  java.net.BindException: Address already in use (Bind failed)
INFO [2017-12-06 15:27:10,048] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 15:27:10,050] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-06 15:27:13,651] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 15:27:13,652] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-06 15:27:19,678] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-06 15:27:19,678] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-06 15:28:53,238] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-06 15:32:07,324] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-06 15:32:07,328] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-07 14:40:33,767] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-07 14:40:41,915] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-07 14:40:41,915] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-07 14:40:41,915] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-07 14:40:42,006] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-07 14:40:42,006] [Main.java:157]  OS: Mac OS X
INFO [2017-12-07 14:40:52,581] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-07 14:40:54,839] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-07 14:40:54,850] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-07 14:40:55,038] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-07 14:41:13,498] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 14:41:13,501] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-07 14:41:35,879] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 14:41:35,881] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-07 14:42:00,919] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 14:42:00,922] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-07 14:42:50,726] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-07 14:46:41,785] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-07 14:54:13,435] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-07 14:54:13,436] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-07 14:54:13,436] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-07 14:54:13,443] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-07 14:54:13,443] [Main.java:157]  OS: Mac OS X
INFO [2017-12-07 14:54:14,570] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-07 14:54:19,446] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-07 14:54:19,458] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-07 14:54:19,514] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-07 15:01:01,290] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:01:01,292] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-07 15:01:01,869] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-07 15:01:07,904] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:01:07,906] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-07 15:05:56,578] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-07 15:05:56,587] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-07 15:07:40,999] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-07 15:07:41,000] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-07 15:07:41,000] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-07 15:07:41,004] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-07 15:07:41,004] [Main.java:157]  OS: Mac OS X
INFO [2017-12-07 15:07:42,721] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-07 15:07:45,541] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-07 15:07:45,549] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-07 15:07:45,590] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-07 15:08:15,906] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:08:15,908] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-07 15:08:20,639] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:08:20,640] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-07 15:08:25,763] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:08:25,763] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-07 15:08:57,008] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-07 15:13:00,318] [MessageUtils.java:74]  Cannot find feature or locus: cd2000r2
INFO [2017-12-07 15:14:42,311] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-07 15:16:00,639] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-07 15:16:00,639] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-07 15:16:00,640] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-07 15:16:00,645] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-07 15:16:00,645] [Main.java:157]  OS: Mac OS X
INFO [2017-12-07 15:16:01,694] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-07 15:16:06,192] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-07 15:16:06,203] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-07 15:16:06,248] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-07 15:17:24,520] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:17:24,522] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-07 15:17:29,599] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:17:29,600] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-07 15:17:35,147] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:17:35,149] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-07 15:18:13,673] [HttpUtils.java:864]  Range-byte request succeeded
INFO [2017-12-07 15:25:46,952] [ShutdownThread.java:47]  Shutting down
INFO [2017-12-07 15:27:04,821] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-07 15:27:04,821] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-07 15:27:04,821] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-07 15:27:04,825] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-07 15:27:04,826] [Main.java:157]  OS: Mac OS X
INFO [2017-12-07 15:27:05,880] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-07 15:27:08,391] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-07 15:27:08,401] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-07 15:27:08,440] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-07 15:27:23,725] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:27:23,727] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-07 15:27:28,124] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:27:28,125] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-07 15:27:33,526] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:27:33,526] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/UN_merged.bam
INFO [2017-12-07 15:28:01,742] [HttpUtils.java:864]  Range-byte request succeeded
ERROR [2017-12-07 15:46:00,314] [AlignmentTileLoader.java:300]  Error loading alignment data
java.util.ConcurrentModificationException
	at java.util.ArrayList.sort(ArrayList.java:1462)
	at org.broad.igv.sam.InsertionManager.processAlignments(InsertionManager.java:146)
	at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:287)
	at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:334)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:309)
	at org.broad.igv.sam.CoverageTrack.load(CoverageTrack.java:187)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:226)
	at java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1626)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
INFO [2017-12-07 15:46:00,315] [MessageUtils.java:74]  <html>Error encountered querying alignments: java.util.ConcurrentModificationException
ERROR [2017-12-07 15:46:39,715] [AlignmentTileLoader.java:300]  Error loading alignment data
java.util.ConcurrentModificationException
	at java.util.ArrayList.sort(ArrayList.java:1462)
	at org.broad.igv.sam.InsertionManager.processAlignments(InsertionManager.java:146)
	at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:287)
	at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:334)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:309)
	at org.broad.igv.sam.CoverageTrack.load(CoverageTrack.java:187)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:226)
	at java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1626)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
INFO [2017-12-07 15:46:39,715] [MessageUtils.java:74]  <html>Error encountered querying alignments: java.util.ConcurrentModificationException
INFO [2017-12-07 15:47:47,576] [ShutdownThread.java:47]  Shutting down
ERROR [2017-12-07 15:47:47,579] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.IllegalStateException: zip file closed
	at java.util.zip.ZipFile.ensureOpen(ZipFile.java:686)
	at java.util.zip.ZipFile.getEntry(ZipFile.java:315)
	at java.util.jar.JarFile.getEntry(JarFile.java:240)
	at java.util.jar.JarFile.getJarEntry(JarFile.java:223)
	at com.sun.deploy.security.DeployURLClassPath$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:48)
	at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:60)
INFO [2017-12-07 15:49:38,164] [Main.java:154]  Startup  IGV Version 2.4.4 11/09/2017 01:52 PM
INFO [2017-12-07 15:49:38,165] [Main.java:155]  Java 1.8.0_151
INFO [2017-12-07 15:49:38,165] [DirectoryManager.java:76]  Fetching user directory... 
INFO [2017-12-07 15:49:38,169] [Main.java:156]  Default User Directory: /Users/kpatrick
INFO [2017-12-07 15:49:38,169] [Main.java:157]  OS: Mac OS X
INFO [2017-12-07 15:49:39,410] [GenomeManager.java:190]  Loading genome: /Users/kpatrick/igv/genomes/mm10.genome
INFO [2017-12-07 15:49:42,660] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2017-12-07 15:49:42,670] [GenomeManager.java:270]  Genome loaded.  id= mm10
INFO [2017-12-07 15:49:42,713] [CommandListener.java:120]  Listening on port 60151
INFO [2017-12-07 15:50:35,664] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:50:35,665] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/ESX_merged.bam
INFO [2017-12-07 15:50:40,991] [IGV.java:1380]  Loading 1 resources.
INFO [2017-12-07 15:50:40,992] [TrackLoader.java:126]  Loading resource, path /Users/kpatrick/Desktop/IGV mouse genome and canonical transcripts/MTB_merged.bam
INFO [2017-12-07 15:51:02,593] [HttpUtils.java:864]  Range-byte request succeeded