IGV continuously crashing

[matteo...@fmach.it]

Dear IGV team and users, I am experiencing a lot of problems with IGV (and other people in my team too).

At the beginning it worked smoothly, with no problem; at some point, on linux ubuntu, it started to give an error when I tried to re-open gff3 files that it was able to open a few weeks before without any problem. The same files were loaded without problems on windows and mac.

Concerning the mac, I freshly installed IGV and yesterday I was able to load my genome and gene predictions, but today it even does not start, crashing after 2-3 seconds after I run it.

I paste the error it is giving today, can you take a look?

INFO [2014-08-04 14:42:01,116]  [DirectoryManager.java:149] [main]  IGV Directory: /Users/matteobrilli/igv

INFO [2014-08-04 14:42:01,116] [DirectoryManager.java:149]  IGV Directory: /Users/matteobrilli/igv

INFO [2014-08-04 14:42:01,126]  [Main.java:85] [main]  Startup  IGV Version 2.3.34 (41)06/19/2014 10:41 PM

INFO [2014-08-04 14:42:01,126]  [Main.java:86] [main]  Java 1.6.0_65

INFO [2014-08-04 14:42:01,126]  [DirectoryManager.java:58] [main]  Fetching user directory... 

INFO [2014-08-04 14:42:01,128]  [Main.java:87] [main]  Default User Directory: /Users/matteobrilli

INFO [2014-08-04 14:42:01,128]  [Main.java:88] [main]  OS: Mac OS X

ERROR [2014-08-04 14:42:02,250]  [DefaultExceptionHandler.java:42] [main]  Unhandled exception

java.lang.IncompatibleClassChangeError: class com.google.common.cache.CacheBuilder$3 has interface com.google.common.base.Ticker as super class

at java.lang.ClassLoader.defineClass1(Native Method)

at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)

at java.lang.ClassLoader.defineClass(ClassLoader.java:621)

at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)

at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)

at java.net.URLClassLoader.access$000(URLClassLoader.java:58)

at java.net.URLClassLoader$1.run(URLClassLoader.java:197)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

at com.google.common.cache.CacheBuilder.<clinit>(CacheBuilder.java:207)

at com.google.common.eventbus.EventBus.<init>(EventBus.java:158)

at com.google.common.eventbus.EventBus.<init>(EventBus.java:173)

at com.google.common.eventbus.AsyncEventBus.<init>(AsyncEventBus.java:61)

at org.broad.igv.ui.panel.ReferenceFrame.getEventBus(ReferenceFrame.java:151)

at org.broad.igv.ui.panel.ReferenceFrame.registerEventBuses(ReferenceFrame.java:144)

at org.broad.igv.ui.panel.ReferenceFrame.<init>(ReferenceFrame.java:120)

at org.broad.igv.ui.panel.FrameManager.getDefaultFrame(FrameManager.java:49)

at org.broad.igv.ui.panel.FrameManager.<clinit>(FrameManager.java:44)

at org.broad.igv.session.Session.<init>(Session.java:46)

at org.broad.igv.ui.IGV.<init>(IGV.java:257)

at org.broad.igv.ui.IGV.createInstance(IGV.java:166)

at org.broad.igv.ui.Main.open(Main.java:224)

at org.broad.igv.ui.Main.main(Main.java:71)

ERROR [2014-08-04 14:42:02,375]  [DefaultExceptionHandler.java:42] [Thread-5]  Unhandled exception

java.lang.NullPointerException

at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1332)

at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2018)

at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:47)

at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:55)

[Jim Robinson]

Thanks for the report.  Could you send us the log for the gff3 problems on linux? 

Also, if possible, please update your Java to 1.7.  

Jim

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[Jim Robinson]

Hi,

How are you installing IGV on the Mac?  Are you using the Mac app bundle, or the "Web Start" buttons on the Downloads page? 

Jim

[Matteo Brilli]

I suspect it is an error related to the text encoding but I was not able to find an encoding that works. It do this loading a gff3 that it was able to open before. It tries to parse a number and it throws a number formatexception for "0.7" which IS a number (for this reason I guess there is a wrong encoding but I am not an expert). Anyway, the very same file was opened on another computer with windows, and yesterday it was fine on my mac (that today gave the error at opening I just sent). I am still trying to understand. This is the error on linux ****

I just updated my JSDK to 1.8, but the error is still happening.

java -version

java version "1.8.0_11"

Java(TM) SE Runtime Environment (build 1.8.0_11-b12)

Java HotSpot(TM) 64-Bit Server VM (build 25.11-b03, mixed mode)

tried both the javaws and .app: same error.

****

The error on linux is:

INFO [2014-08-04 16:07:55,685]  [DirectoryManager.java:149] [main]  IGV Directory: /home/matteo/igv
INFO [2014-08-04 16:07:55,685] [DirectoryManager.java:149]  IGV Directory: /home/matteo/igv
INFO [2014-08-04 16:07:55,688]  [Main.java:85] [main]  Startup  IGV Version 2.3.34 (41)06/19/2014 10:41 PM
INFO [2014-08-04 16:07:55,689]  [Main.java:86] [main]  Java 1.6.0_31
INFO [2014-08-04 16:07:55,689]  [DirectoryManager.java:58] [main]  Fetching user directory... 
INFO [2014-08-04 16:07:55,824]  [Main.java:87] [main]  Default User Directory: /home/matteo
INFO [2014-08-04 16:07:55,824]  [Main.java:88] [main]  OS: Linux
INFO [2014-08-04 16:08:07,821]  [GenomeManager.java:130] [main]  Loading genome: Scaffolds.fasta
INFO [2014-08-04 16:08:08,109]  [GenomeManager.java:174] [main]  Genome loaded.  id= Scaffolds.fasta
INFO [2014-08-04 16:08:08,682]  [CommandListener.java:85] [Thread-6]  Listening on port 60151
INFO [2014-08-04 16:08:24,918]  [IGV.java:1640] [pool-1-thread-6]  Loading 1 resources.
INFO [2014-08-04 16:08:24,919]  [TrackLoader.java:112] [pool-1-thread-6]  Loading resource, pathXXX_final_AUGUSTUS_onRK69_with_ALL_HINTS.gff3
INFO [2014-08-04 16:08:27,427]  [MessageUtils.java:60] [pool-1-thread-6]  java.lang.NumberFormatException: For input string: "0.7"
ERROR [2014-08-04 16:09:39,602]  [TrackLoader.java:248] [pool-1-thread-6]  Error parsing line at byte position: org.broad.tribble.readers.LineIteratorImpl@1887b104, for input source: XXX_final_AUGUSTUS_onRK69_with_ALL_HINTS.gff3
org.broad.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: org.broad.tribble.readers.LineIteratorImpl@1887b104, for input source: XXX_final_AUGUSTUS_onRK69_with_ALL_HINTS.gff3
    at org.broad.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:302)
    at org.broad.tribble.TribbleIndexedFeatureReader$WFIterator.<init>(TribbleIndexedFeatureReader.java:256)
    at org.broad.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:223)
    at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:55)
    at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.<init>(TribbleFeatureSource.java:298)
    at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.<init>(TribbleFeatureSource.java:284)
    at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:88)
    at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:60)
    at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:366)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:129)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:98)
    at org.broad.igv.ui.IGV.load(IGV.java:1747)
    at org.broad.igv.ui.IGV$11.run(IGV.java:1661)
    at org.broad.igv.ui.IGV.loadResources(IGV.java:1674)
    at org.broad.igv.ui.IGV$5.run(IGV.java:724)
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:701)
Caused by: java.lang.NumberFormatException: For input string: "0.7"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:481)
    at java.lang.Integer.parseInt(Integer.java:514)
    at org.broad.igv.feature.tribble.UCSCGeneTableCodec.decode(UCSCGeneTableCodec.java:114)
    at org.broad.igv.feature.tribble.UCSCGeneTableCodec.decode(UCSCGeneTableCodec.java:27)
    at org.broad.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:73)
    at org.broad.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:35)
    at org.broad.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:288)
    ... 20 more
ERROR [2014-08-04 16:09:39,606]  [IGV.java:1665] [pool-1-thread-6]  Error loading track
org.broad.igv.exceptions.DataLoadException: Error parsing line at byte position: org.broad.tribble.readers.LineIteratorImpl@1887b104, for input source: XXX_final_AUGUSTUS_onRK69_with_ALL_HINTS.gff3
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:250)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:98)
    at org.broad.igv.ui.IGV.load(IGV.java:1747)
    at org.broad.igv.ui.IGV$11.run(IGV.java:1661)
    at org.broad.igv.ui.IGV.loadResources(IGV.java:1674)
    at org.broad.igv.ui.IGV$5.run(IGV.java:724)
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:701)
INFO [2014-08-04 16:09:39,607]  [MessageUtils.java:60] [pool-1-thread-6]  Error loading XXX_final_AUGUSTUS_onRK69_with_ALL_HINTS.gff3: Error parsing line at byte position: org.broad.tribble.readers.LineIteratorImpl@1887b104, for input source: XXX_final_AUGUSTUS_onRK69_with_ALL_HINTS.gff3

[Jim Robinson]

Hi Matteo,

You are experiencing 2 unrelated errors.    The MacOS error reported in your previous post is odd, it looks like you have an incompatible version of Google's "guava" jar file in your path.   This error can sometimes happen with Java Web Start, clearing the Java cache will often resolve it.   However, if you get this error using the .app bundle I do not have an explanation.   Can you please confirm that you experience the  following exception on your Mac when running from the .app bundle?    Note this is not the gff3 problem, it is unrelated:   'Unhandled exceptionjava.lang.IncompatibleClassChangeError: class com.google.common.cache.CacheBuilder$3 has interface com.google.common.base.Ticker as super class

I will need to see your gff3 file to help with the second error.  0.7 is a number, but it is not an integer,  so if this appears for example in the position column it would cause an error.   Please attach the gff3 file, or alternatively you can email it to igv-team (at) broadinstitute.org.

Jim

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[matteo...@fmach.it]

Yes, the two errors are unrelated. What is not unrelated is maybe their synchrony..I needed IGV and both my installations are systematically crashing.

I'll provide then the info you need for the linux error (I'll send the gff to the igv team by e-mail).

For the mac one. I tried

javaws -clearchache

and then ran again the jnlp file. Still the same (as you said, guava related) error.

The very same happens using the .app (just tried for the two 1E+05th time). Well, I don't see the error running the .command (but the program crashes); I am able to see the error by running

java -Xmx2000m -jar igv.jar

Now, what is strange is that two days ago this incompatibility with my guava library did not happened (but I don't remember if I was running through the javaws or the .app), and without touching anything yesterday I started to get that error. I was using guava-r09.jar, now I tried to download guava-17.0.jar but no luck; the error is still coming out.

What version you used when testing IGV?

Now I just downloaded the jnlp file for IGV 2.1 and...it works! I am also able to load the gff files that caused the error on linux.

[Jim Robinson]

Hi Matteo,

I don't know what to say,  I have MacOS as do hundreds of local users here, so usually we find any obvious errors quickly.   If you send me the entire igv.log file from the problematic machines I will look through them for any clues.  You can send them to the same igv-team email.

Jim

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