Problems with java.lang.ArrayIndexOutOfBoundsException

Woody Lin

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Jun 7, 2017, 12:50:44 PM6/7/17

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Hi all,

I am using the latest version of JAVA (Java 8 update 131) and the latest version of IGV (IGV_2.3.93). I can't put .bed or .gtf files in the IGV browser. Could someone please help?

Thanks,

Woody

James Robinson

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Jun 7, 2017, 1:56:53 PM6/7/17

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Can you attach a bed file that is giving you this problem? Also, your igv.log file would be helpful. Its located in an "igv" folder in your home directory.

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Woody Lin

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Jun 9, 2017, 9:36:41 AM6/9/17

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Hi Jim,

It is not the problem of bed file. It happens even if I load genome annotation from server (resulted in blank annotation). I attached the first 100 lines of the gtf file. Below is the log:

INFO [2017-06-09 09:20:12,329] [Main.java:135]  Startup  IGV Version 2.3.93 (151)05/15/2017 06:11 PM
INFO [2017-06-09 09:20:12,333] [Main.java:136]  Java 1.8.0_131
INFO [2017-06-09 09:20:12,333] [DirectoryManager.java:72]  Fetching user directory... 
INFO [2017-06-09 09:20:12,894] [Main.java:137]  Default User Directory: /Users/xuser
INFO [2017-06-09 09:20:12,894] [Main.java:138]  OS: Mac OS X
INFO [2017-06-09 09:20:15,791] [GenomeManager.java:145]  Loading genome: /Users/xuser/igv/genomes/hg38.genome
INFO [2017-06-09 09:20:17,412] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-06-09 09:20:17,476] [CommandListener.java:106]  Listening on port 60151
INFO [2017-06-09 09:20:53,787] [IGV.java:1701]  Loading 1 resources.
INFO [2017-06-09 09:20:53,788] [TrackLoader.java:126]  Loading resource, path https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/genes/Homo_sapiens.GRCh38.80.sorted.gtf.gz
INFO [2017-06-09 09:20:54,235] [HttpUtils.java:856]  Range-byte request succeeded
INFO [2017-06-09 09:21:30,778] [IGV.java:1701]  Loading 1 resources.
INFO [2017-06-09 09:21:30,778] [TrackLoader.java:126]  Loading resource, path https://s3.amazonaws.com/igv.broadinstitute.org/data/hg38/gencode.v24.annotation.sorted.gtf.gz
INFO [2017-06-09 09:25:36,438] [ShutdownThread.java:51]  Shutting down
INFO [2017-06-09 09:25:36,441] [ShutdownThread.java:51]  Shutting down
INFO [2017-06-09 09:27:05,298] [Main.java:135]  Startup  IGV Version 2.3.93 (151)05/15/2017 06:11 PM
INFO [2017-06-09 09:27:05,298] [Main.java:136]  Java 1.8.0_131
INFO [2017-06-09 09:27:05,299] [DirectoryManager.java:72]  Fetching user directory... 
INFO [2017-06-09 09:27:05,302] [Main.java:137]  Default User Directory: /Users/xuser
INFO [2017-06-09 09:27:05,302] [Main.java:138]  OS: Mac OS X
INFO [2017-06-09 09:27:06,328] [GenomeManager.java:145]  Loading genome: /Users/xuser/igv/genomes/hg38.genome
INFO [2017-06-09 09:27:07,502] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-06-09 09:27:07,552] [CommandListener.java:106]  Listening on port 60151
INFO [2017-06-09 09:27:16,996] [TrackLoader.java:126]  Loading resource, path /Users/xuser/Documents/Homo_sapiens.GRCh38.87.sorted.gtf
ERROR [2017-06-09 09:27:17,104] [DataPanelContainer.java:223]  java.awt.datatransfer.UnsupportedFlavorException: Unicode String
INFO [2017-06-09 09:27:19,434] [MessageUtils.java:74]  Error loading features for interval: chr17:76534114-76937411 <br>java.lang.ArrayIndexOutOfBoundsException: -116466
ERROR [2017-06-09 09:29:18,251] [FeatureTrack.java:926]  Error loading features for interval: chr17:76534114-76937411 <br>java.lang.ArrayIndexOutOfBoundsException: -116466
java.lang.ArrayIndexOutOfBoundsException: -116466
	at java.util.ArrayList.elementData(ArrayList.java:418)
	at java.util.ArrayList.get(ArrayList.java:431)
	at htsjdk.tribble.index.linear.LinearIndex$ChrIndex.getBlocks(LinearIndex.java:209)
	at htsjdk.tribble.index.AbstractIndex.getBlocks(AbstractIndex.java:314)
	at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:263)
	at org.broad.igv.feature.tribble.CachingFeatureReader.queryRaw(CachingFeatureReader.java:73)
	at org.broad.igv.feature.AbstractCacher.loadTiles(AbstractCacher.java:198)
	at org.broad.igv.feature.AbstractCacher.getBins(AbstractCacher.java:172)
	at org.broad.igv.feature.AbstractCacher.queryCached(AbstractCacher.java:102)
	at org.broad.igv.feature.tribble.CachingFeatureReader.query(CachingFeatureReader.java:104)
	at org.broad.igv.track.TribbleFeatureSource$IndexedFeatureSource.getFeatures(TribbleFeatureSource.java:198)
	at org.broad.igv.track.GFFFeatureSource.getFeatures(GFFFeatureSource.java:65)
	at org.broad.igv.track.FeatureTrack$1.run(FeatureTrack.java:904)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)
INFO [2017-06-09 09:29:19,148] [ShutdownThread.java:51]  Shutting down
INFO [2017-06-09 09:29:19,152] [ShutdownThread.java:51]  Shutting down

Jim Robinson於 2017年6月7日星期三 UTC-4下午1時56分53秒寫道：

Can you attach a bed file that is giving you this problem? Also, your igv.log file would be helpful. Its located in an "igv" folder in your home directory.

On Wed, Jun 7, 2017 at 9:50 AM, Woody Lin <woody...@gmail.com> wrote:

Hi all,

I am using the latest version of JAVA (Java 8 update 131) and the latest version of IGV (IGV_2.3.93). I can't put .bed or .gtf files in the IGV browser. Could someone please help?

Thanks,
Woody

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head100_Homo_sapiens.GRCh38.87.sorted.gtf

James Robinson

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Jun 9, 2017, 11:07:41 AM6/9/17

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This is odd as I can load both files you reference using 2.3.93 (see screenshot). The error from your log would only occur with igv indexed files (files with a corresponding .idx file).

However, before exploring that let's focus on the server loaded file since we both have access.

I don't see any error for the server loaded file. It is normal that an indexed track is "blank" until you zoom in, but it should display a "'zoom in to see features" message. Could you try loading just the server file and zooming in, for example to chr1:1-546,457, and send a screenshot of what you see?

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Woody Lin

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Jun 9, 2017, 11:09:03 AM6/9/17

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That's what I am so confused right now as well. My friend's computer works, but only my computer has such error message.

Woody

Jim Robinson於 2017年6月9日星期五 UTC-4上午11時07分41秒寫道：

Woody Lin

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Jun 9, 2017, 11:22:47 AM6/9/17

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Hi Jim,

I fixed the problem by changing "Default visibility window" to 0. It was 2000000. I don't know what the number means.

Thanks,

Woody

Woody Lin於 2017年6月9日星期五 UTC-4上午11時09分03秒寫道：

James Robinson

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Jun 9, 2017, 11:46:31 AM6/9/17

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OK thanks, that's helpful, I will look into this further.

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Woody Lin

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Jun 9, 2017, 12:36:03 PM6/9/17

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Hi Jim,

Could you please tell me how to increase the size that IGV can show alignments? The default seems to be 20~30 kb. I hope to display a larger range like 100 kb.

Thanks,

Woody

Jim Robinson於 2017年6月9日星期五 UTC-4上午11時46分31秒寫道：

James Robinson

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Jun 9, 2017, 12:37:53 PM6/9/17

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Set the visibility window in the alignment preferences (View > Preferences > Alignments tab) to whatever you want, but larger values require more memory of course. I generally have mine set to 200.

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Woody Lin

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Jun 9, 2017, 1:19:58 PM6/9/17

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Thanks!

Woody

Jim Robinson於 2017年6月9日星期五 UTC-4下午12時37分53秒寫道：

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