java.lang.NullPointerException when loading saved IGV session

[Dan Santos]

Hello,

I am using IGV_2.3.80 and OS X 10.11.16. I have a recurring problem with a java.lang.NullPointerException when trying to load a saved session from a server I'm connected to. The same thing happens if I try to load a genome from the same server. On several occasions I've had to re-create the .genome file and re-load all of my tracks and preferences (saved as a new session), which usually works fine for several weeks until eventually giving this error. There should be no problems accessing the files from my machine (I am connected via SMB, and can browse the server directories in the Finder). I've attached the log file. Thanks,

Dan

~ ~ ~

INFO [2016-08-18 18:57:48,380] [Main.java:133]  Startup  IGV Version 2.3.80 (119)08/04/2016 05:06 PM

INFO [2016-08-18 18:57:48,380] [Main.java:134]  Java 1.8.0_101

INFO [2016-08-18 18:57:48,380] [DirectoryManager.java:72]  Fetching user directory... 

INFO [2016-08-18 18:57:49,005] [Main.java:135]  Default User Directory: /Users/Dan

INFO [2016-08-18 18:57:49,005] [Main.java:136]  OS: Mac OS X

INFO [2016-08-18 18:57:54,759] [GenomeManager.java:145]  Loading genome: /Users/Dan/igv/genomes/sacCer3.genome

INFO [2016-08-18 18:57:55,113] [GenomeManager.java:192]  Genome loaded.  id= sacCer3

INFO [2016-08-18 18:57:55,182] [CommandListener.java:106]  Listening on port 60151

ERROR [2016-08-18 18:58:16,896] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro3) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro3.genome  panTro3

ERROR [2016-08-18 18:58:16,896] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro4) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro4.genome  panTro4

INFO [2016-08-18 18:58:16,972] [GenomeManager.java:145]  Loading genome: null

ERROR [2016-08-18 18:58:16,974] [IGVCommandBar.java:285]  Error initializing genome

java.lang.NullPointerException

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:156)

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129)

at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250)

at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)

at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:297)

at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83)

at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:308)

at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1258)

at javax.swing.JComboBox.setSelectedItem(JComboBox.java:586)

at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:541)

at org.broad.igv.ui.IGV.selectGenomeFromList(IGV.java:475)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:396)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)

at org.broad.igv.ui.IGV$10.run(IGV.java:1442)

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 [2016-08-18 18:58:16,986] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;/Volumes/dsantos/meiosis/igv_sessions/rna_rpf_norm_centermap.xml<br>null

java.lang.NullPointerException

at java.io.File.<init>(File.java:277)

at org.broad.igv.util.FileUtils.getAbsolutePath(FileUtils.java:371)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:400)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)

at org.broad.igv.ui.IGV$10.run(IGV.java:1442)

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 [2016-08-18 18:58:16,995] [MessageUtils.java:74]  <html>Unexpected error: java.lang.NullPointerException.<br>See igv.log for more details

ERROR [2016-08-18 18:58:20,325] [LongRunningTask.java:75]  Exception running task

java.lang.RuntimeException: java.lang.NullPointerException

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)

at org.broad.igv.ui.IGV$10.run(IGV.java:1442)

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.NullPointerException

at java.io.File.<init>(File.java:277)

at org.broad.igv.util.FileUtils.getAbsolutePath(FileUtils.java:371)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:400)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)

... 6 more

 

[Jim Robinson]

This might be hard to reproduce, but can you attach a session file that is causing this problem?  I won't be able to load it, but maybe something will jump out by inspection.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/fba2e8b1-00a4-4074-a443-0fed1c83264d%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Dan Santos]

Session file is attached. Thanks,

Dan

[Jim Robinson]

And this one fails with the NPE?

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/6da6c298-0996-4f39-bb66-4dd69a2681cb%40googlegroups.com.

[Dan Santos]

Yes, this is the exact file that fails with a NPE. I get the same error if I open IGV and try to load a genome from the drop-down menu, if that genome file is stored on the server. The default yeast file, however, loads ok. I believe this file is stored locally on my machine.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/6da6c298-0996-4f39-bb66-4dd69a2681cb%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/q_Lh4EJprRA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/2d513642-b6de-0b65-4a6a-589e5a58e1c8%40broadinstitute.org.

[Jim Robinson]

Could you send the stack trace (in igv.log) for he error when you try to load the genome?  Probably same root cause, but it would be from a different place in the code.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAPDvTy5W5YqT%2B3qWychJm2TH%2B3MTfWrY21tKwpxzhZrprh4ZWQ%40mail.gmail.com.

[Jim Robinson]

Also, verify that from a command prompt you can do this and see the contents of the file

more /Volumes/dsantos/meiosis/igv_sessions/rna_rpf_norm_centermap.xml

On 8/18/16 9:45 PM, Dan Santos wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAPDvTy5W5YqT%2B3qWychJm2TH%2B3MTfWrY21tKwpxzhZrprh4ZWQ%40mail.gmail.com.

[Dan Santos]

The 'more' command seemed to work fine

Here's the log file when I launched IGV and tried to load a new genome, after the default sacCer3 genome loaded no problem (this time I didn't get the NPE - sometimes it loads with a "blank" display (ie. no Gene tracks, see attached image), and only gives the NPE when I try to zoom in. Other times it loads the blank display and allows me to zoom, which is what happened this time). However if I try to load the saved session it always gives a NPE.

INFO [2016-08-19 10:23:37,637] [Main.java:133]  Startup  IGV Version 2.3.80 (119)08/04/2016 05:06 PM

INFO [2016-08-19 10:23:37,638] [Main.java:134]  Java 1.8.0_101

INFO [2016-08-19 10:23:37,638] [DirectoryManager.java:72]  Fetching user directory... 

INFO [2016-08-19 10:23:37,960] [Main.java:135]  Default User Directory: /Users/Dan

INFO [2016-08-19 10:23:37,961] [Main.java:136]  OS: Mac OS X

INFO [2016-08-19 10:23:41,624] [GenomeManager.java:145]  Loading genome: /Users/Dan/igv/genomes/sacCer3.genome

INFO [2016-08-19 10:23:41,975] [GenomeManager.java:192]  Genome loaded.  id= sacCer3

INFO [2016-08-19 10:23:42,050] [CommandListener.java:106]  Listening on port 60151

ERROR [2016-08-19 10:23:47,464] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro3) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro3.genome  panTro3

ERROR [2016-08-19 10:23:47,464] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro4) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro4.genome  panTro4

INFO [2016-08-19 10:23:47,539] [GenomeManager.java:145]  Loading genome: null

ERROR [2016-08-19 10:23:47,541] [IGVCommandBar.java:285]  Error initializing genome

java.lang.NullPointerException

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:156)

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129)

at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250)

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)

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/6da6c298-0996-4f39-bb66-4dd69a2681cb%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/q_Lh4EJprRA/unsubscribe.

To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/2d513642-b6de-0b65-4a6a-589e5a58e1c8%40broadinstitute.org.

For more options, visit https://groups.google.com/d/optout.

[Dan Santos]

Another confusing thing that I just realized: when trying to load a different saved session, stored on the same server, it works fine

[Jim Robinson]

Yea I don't get this at all.  We don't have Samba here so its hard to reproduce.  If it continues could you switch to the "snapshot" build?  If the errors persist there I can add more logging statements along the path and maybe narrow this down.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/92fc16a1-7a6f-441e-8063-5e13390a6fd7%40googlegroups.com.

[Dan Santos]

Ok, switched to the snapshot build and still getting the error. Here's the log. Thanks for your continued help on this!

INFO [2016-08-19 11:11:18,335] [Main.java:135]  Startup  IGV Version Snapshot (688 (688))08/19/2016 11:45 AM

INFO [2016-08-19 11:11:18,336] [Main.java:136]  Java 1.8.0_101

INFO [2016-08-19 11:11:18,337] [DirectoryManager.java:72]  Fetching user directory... 

INFO [2016-08-19 11:11:18,730] [Main.java:137]  Default User Directory: /Users/Dan

INFO [2016-08-19 11:11:18,730] [Main.java:138]  OS: Mac OS X

INFO [2016-08-19 11:11:21,483] [GenomeManager.java:145]  Loading genome: /Users/Dan/Documents/Genome/From_genometools_rev765/S_cerevisiae_r64.genome

INFO [2016-08-19 11:11:22,686] [GenomeManager.java:192]  Genome loaded.  id= S. cerevisiae r64

INFO [2016-08-19 11:11:22,782] [CommandListener.java:106]  Listening on port 60151

ERROR [2016-08-19 11:11:48,264] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro3) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro3.genome  panTro3

ERROR [2016-08-19 11:11:48,264] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro4) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro4.genome  panTro4

INFO [2016-08-19 11:11:48,336] [GenomeManager.java:145]  Loading genome: null

ERROR [2016-08-19 11:11:48,338] [IGVCommandBar.java:284]  Error initializing genome

java.lang.NullPointerException

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:156)

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129)

at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:249)

at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)

at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:296)

at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83)

at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:307)

at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1258)

at javax.swing.JComboBox.setSelectedItem(JComboBox.java:586)

at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:540)

at org.broad.igv.ui.IGV.selectGenomeFromList(IGV.java:484)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:396)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1480)

at org.broad.igv.ui.IGV$10.run(IGV.java:1449)

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 [2016-08-19 11:11:48,350] [IGV.java:1514]  Error loading session session : <br>&nbsp;&nbsp;/Volumes/dsantos/meiosis/igv_sessions/rna_rpf_norm_centermap.xml<br>null

java.lang.NullPointerException

at java.io.File.<init>(File.java:277)

at org.broad.igv.util.FileUtils.getAbsolutePath(FileUtils.java:373)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:400)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1480)

at org.broad.igv.ui.IGV$10.run(IGV.java:1449)

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 [2016-08-19 11:11:48,353] [MessageUtils.java:74]  <html>Unexpected error: java.lang.NullPointerException.<br>See igv.log for more details

[Jim Robinson]

OK, if you can reinstall the "snapshot" build and try again we should get more information, I added some logging statements to the "Load genome" code.   Let's start with that one, and deal with session after.

After trying it post the log contents.

On 8/18/16 9:45 PM, Dan Santos wrote:

[Dan Santos]

Here it is (tried to load genome from drop-down menu, got a blank screen, no NPE upon zooming):

INFO [2016-08-19 13:49:32,854] [Main.java:135]  Startup  IGV Version Snapshot (690 (690))08/19/2016 03:26 PM

INFO [2016-08-19 13:49:32,855] [Main.java:136]  Java 1.8.0_101

INFO [2016-08-19 13:49:32,855] [DirectoryManager.java:72]  Fetching user directory... 

INFO [2016-08-19 13:49:33,421] [Main.java:137]  Default User Directory: /Users/Dan

INFO [2016-08-19 13:49:33,421] [Main.java:138]  OS: Mac OS X

INFO [2016-08-19 13:49:39,660] [GenomeManager.java:145]  Loading genome: /Users/Dan/Documents/Genome/From_genometools_rev765/S_cerevisiae_r64.genome

INFO [2016-08-19 13:49:41,022] [GenomeManager.java:192]  Genome loaded.  id= S. cerevisiae r64

INFO [2016-08-19 13:49:41,131] [CommandListener.java:106]  Listening on port 60151

ERROR [2016-08-19 13:50:10,466] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro3) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro3.genome  panTro3

ERROR [2016-08-19 13:50:10,466] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro4) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro4.genome  panTro4

INFO [2016-08-19 13:50:10,538] [GenomeManager.java:145]  Loading genome: null

ERROR [2016-08-19 13:50:10,540] [IGVCommandBar.java:284]  Error initializing genome

java.lang.NullPointerException

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:156)

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129)

at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:249)

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)

[Dan Santos]

Here's after trying to load the problematic session file:

INFO [2016-08-19 13:55:54,183] [Main.java:135]  Startup  IGV Version Snapshot (690 (690))08/19/2016 03:26 PM

INFO [2016-08-19 13:55:54,183] [Main.java:136]  Java 1.8.0_101

INFO [2016-08-19 13:55:54,183] [DirectoryManager.java:72]  Fetching user directory... 

INFO [2016-08-19 13:55:54,557] [Main.java:137]  Default User Directory: /Users/Dan

INFO [2016-08-19 13:55:54,558] [Main.java:138]  OS: Mac OS X

INFO [2016-08-19 13:55:57,252] [GenomeManager.java:145]  Loading genome: /Users/Dan/Documents/Genome/From_genometools_rev765/S_cerevisiae_r64.genome

INFO [2016-08-19 13:55:58,410] [GenomeManager.java:192]  Genome loaded.  id= S. cerevisiae r64

INFO [2016-08-19 13:55:58,509] [CommandListener.java:106]  Listening on port 60151

ERROR [2016-08-19 13:56:11,068] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro3) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro3.genome  panTro3

ERROR [2016-08-19 13:56:11,069] [GenomeManager.java:812]  Found invalid server genome list record: Chimp (panTro4) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro4.genome  panTro4

INFO [2016-08-19 13:56:11,140] [GenomeManager.java:145]  Loading genome: null

ERROR [2016-08-19 13:56:11,141] [IGVCommandBar.java:284]  Error initializing genome

java.lang.NullPointerException

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:156)

at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129)

at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:249)

at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)

at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:296)

at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83)

at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:307)

at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1258)

at javax.swing.JComboBox.setSelectedItem(JComboBox.java:586)

at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:540)

at org.broad.igv.ui.IGV.selectGenomeFromList(IGV.java:484)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:396)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1484)

at org.broad.igv.ui.IGV$10.run(IGV.java:1453)

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 [2016-08-19 13:56:11,154] [IGV.java:1518]  Error loading session session : <br>&nbsp;&nbsp;/Volumes/dsantos/meiosis/igv_sessions/rna_rpf_norm_centermap.xml<br>null

java.lang.NullPointerException

at java.io.File.<init>(File.java:277)

at org.broad.igv.util.FileUtils.getAbsolutePath(FileUtils.java:373)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:400)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1484)

at org.broad.igv.ui.IGV$10.run(IGV.java:1453)

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 [2016-08-19 13:56:11,156] [MessageUtils.java:74]  <html>Unexpected error: java.lang.NullPointerException.<br>See igv.log for more details

ERROR [2016-08-19 13:56:12,771] [LongRunningTask.java:75]  Exception running task

java.lang.RuntimeException: java.lang.NullPointerException

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1519)

at org.broad.igv.ui.IGV$10.run(IGV.java:1453)

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.NullPointerException

at java.io.File.<init>(File.java:277)

at org.broad.igv.util.FileUtils.getAbsolutePath(FileUtils.java:373)

at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:400)

at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:324)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1484)

... 6 more

[Jim Robinson]

Could you try loading it from the Genomes menu ("Load from file")?  That's where I put the logging statements.   In the meantime I'll add logging for the pulldown list for the next round.

You can delete igv.log before starting up,  to be sure we're getting current messages.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/7175f5e8-4dc3-4c26-88ec-2faf6ca7d3d2%40googlegroups.com.

[Jim Robinson]

ALso, could I see this file?

~/igv/genomes/user-defined-genomes.txt

On 8/19/16 1:53 PM, Dan Santos wrote:

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/7175f5e8-4dc3-4c26-88ec-2faf6ca7d3d2%40googlegroups.com.

[Dan Santos]

Wow, that seems to have done the trick. After going to Genomes>Load From File, the genome loaded fine. I then tried to open my session and that worked as well. This is all after deleting the log file but I doubt that could have been it...? The non-snapshot of IGV is working properly now, too. The log is below. Thanks!!

INFO [2016-08-19 15:19:50,751] [Main.java:135]  Startup  IGV Version Snapshot (690 (690))08/19/2016 03:26 PM

INFO [2016-08-19 15:19:50,752] [Main.java:136]  Java 1.8.0_101

INFO [2016-08-19 15:19:50,752] [DirectoryManager.java:72]  Fetching user directory... 

INFO [2016-08-19 15:19:51,254] [Main.java:137]  Default User Directory: /Users/Dan

INFO [2016-08-19 15:19:51,254] [Main.java:138]  OS: Mac OS X

INFO [2016-08-19 15:19:56,016] [GenomeManager.java:145]  Loading genome: /Users/Dan/Documents/Genome/From_genometools_rev765/S_cerevisiae_r64.genome

INFO [2016-08-19 15:19:57,145] [GenomeManager.java:192]  Genome loaded.  id= S. cerevisiae r64

INFO [2016-08-19 15:19:57,241] [CommandListener.java:106]  Listening on port 60151

INFO [2016-08-19 15:20:50,894] [IGV.java:641]  Loading genome: file.name=SK1 rebuild.genome  file.path=/Volumes/dsantos/igv/genomes/SK1 rebuild.genome  file.absolutePath=/Volumes/dsantos/igv/genomes/SK1 rebuild.genome

INFO [2016-08-19 15:20:51,289] [GenomeManager.java:145]  Loading genome: /Volumes/dsantos/igv/genomes/SK1 rebuild.genome

INFO [2016-08-19 15:20:51,574] [GenomeManager.java:192]  Genome loaded.  id= SK1 rebuild

INFO [2016-08-19 15:21:16,669] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_rc.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_rc.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_rc.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_fw.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_rc.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_rc.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_fw.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_rc.tdf

INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_fw.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_fw.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_fw.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_fw.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_fw.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_rc.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_rc.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_fw.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_fw.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_fw.tdf

INFO [2016-08-19 15:21:16,669] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_fw.tdf

INFO [2016-08-19 15:21:16,669] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_rc.tdf

INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_rc.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_rc.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_rc.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_rc.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_fw.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_rc.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_rc.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_rc.tdf

INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_fw.tdf

INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_fw.tdf

INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_fw.tdf

INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_fw.tdf

INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/libraries/SK1_sanger/SK1_sanger_26_2_crossmap.bed

INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_rc.tdf

INFO [2016-08-19 15:21:16,671] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_fw.tdf

INFO [2016-08-19 15:21:16,671] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_fw.tdf

INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_rc.tdf

INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_fw.tdf

INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_fw.tdf

INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_rc.tdf

INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_rc.tdf

INFO [2016-08-19 15:23:04,835] [Main.java:133]  Startup  IGV Version 2.3.80 (119)08/04/2016 05:06 PM

INFO [2016-08-19 15:23:04,861] [Main.java:134]  Java 1.8.0_101

INFO [2016-08-19 15:23:04,861] [DirectoryManager.java:72]  Fetching user directory... 

INFO [2016-08-19 15:23:05,384] [Main.java:135]  Default User Directory: /Users/Dan

INFO [2016-08-19 15:23:05,385] [Main.java:136]  OS: Mac OS X

INFO [2016-08-19 15:23:12,614] [GenomeManager.java:145]  Loading genome: /Volumes/dsantos/igv/genomes/SK1 rebuild.genome

INFO [2016-08-19 15:23:13,368] [GenomeManager.java:192]  Genome loaded.  id= SK1 rebuild

ERROR [2016-08-19 15:23:13,379] [ReferenceFrame.java:682]  Null chromosome: 

ERROR [2016-08-19 15:23:13,519] [CommandListener.java:124]  java.net.BindException: Address already in use

INFO [2016-08-19 15:23:26,270] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_rc.tdf

INFO [2016-08-19 15:23:26,277] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_rc.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_rc.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_fw.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_rc.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_rc.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_fw.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_rc.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_fw.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_fw.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_fw.tdf

INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_fw.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_fw.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_rc.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_rc.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_fw.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_fw.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_fw.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_rc.tdf

INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_rc.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_rc.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_rc.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_fw.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_rc.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_rc.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_rc.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_fw.tdf

INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/libraries/SK1_sanger/SK1_sanger_26_2_crossmap.bed

INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_rc.tdf

INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_fw.tdf

INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_fw.tdf

INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_fw.tdf

INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_rc.tdf

INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_fw.tdf

INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_fw.tdf

INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_fw.tdf

INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_rc.tdf

INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_rc.tdf

INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_fw.tdf

INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_fw.tdf

INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120]  Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_rc.tdf

[Dan Santos]

Here's the user-defined-genomes file.

[Jim Robinson]

Is this after the fix?  I was going to check the path to the .genome file, to see if anything looked amis.  If this recurs in the future I think that's where we need to look.

BTW you don't have to create .genome files,  the path to the fasta itself can be substituted.  You need .genome files to automatically load the annotations, and cytobands if they exist, but they aren't required.

On 8/19/16 3:27 PM, Dan Santos wrote:

Here's the user-defined-genomes file.

[Dan Santos]

Yeah, the file I uploaded was after things got fixed. I created the genome file because I have some custom annotations, etc. Thanks again for all of your help. If this happens again I'll start by trying the Genomes>Load trick, and if that doesn't work I'll post a new message.

Best,

Dan