When browsing bam file: "Error: java.util.concurrent.CompletionException: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1" #506

winni2k · 2018-01-14T15:40:59Z

I have previously mentioned this error in #499 and #277, but here is a complete report with a small test case: igv_test_case.tar.gz

This bam file was created by mapping all the contigs in one percent of the P. abies coding sequence to itself.

When I open igv 2.4.5 (installed using homebrew) on my mac running MacOS 10.11.6, and when I load the genome Pabies1.0-all-cds.1pc.fna, and I load the file Pabies1.0-all-cds.1pc.bam, and I navigate to the first contig, and then I navigate to the second contig, and then I navigate to the third contig, then my mouse turns into a blue ball that sort of turns, and I never see any data, and the following error appears in my console:

WARN [2018-01-17 22:59:00,731]  [Globals.java:138] [AWT-EventQueue-0]  Development mode is enabled
INFO [2018-01-17 22:59:00,769]  [DirectoryManager.java:171] [AWT-EventQueue-0]  IGV Directory: /Users/winni/igv
INFO [2018-01-17 22:59:00,769] [DirectoryManager.java:171]  IGV Directory: /Users/winni/igv
INFO [2018-01-17 22:59:00,773]  [Main.java:154] [AWT-EventQueue-0]  Startup  IGV Version 2.4.5 12/14/2017 01:18 AM
INFO [2018-01-17 22:59:00,774]  [Main.java:155] [AWT-EventQueue-0]  Java 1.8.0_31
INFO [2018-01-17 22:59:00,774]  [DirectoryManager.java:76] [AWT-EventQueue-0]  Fetching user directory... 
INFO [2018-01-17 22:59:00,971]  [Main.java:156] [AWT-EventQueue-0]  Default User Directory: /Users/winni
INFO [2018-01-17 22:59:00,972]  [Main.java:157] [AWT-EventQueue-0]  OS: Mac OS X


INFO [2018-01-17 22:59:15,868]  [GenomeManager.java:182] [pool-2-thread-1]  Loading genome: /Volumes/mac-3/home/to_be_backupped_unsensitive/Projects/olof/spruce/data/DAL19_sequences.fa
INFO [2018-01-17 22:59:15,887]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2018-01-17 22:59:16,751]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2018-01-17 22:59:16,764]  [GenomeManager.java:271] [pool-2-thread-1]  Genome loaded.  id= /Volumes/mac-3/home/to_be_backupped_unsensitive/Projects/olof/spruce/data/DAL19_sequences.fa
INFO [2018-01-17 22:59:16,902]  [CommandListener.java:120] [Thread-7]  Listening on port 60151
INFO [2018-01-17 22:59:33,870]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2018-01-17 22:59:33,871]  [GenomeComboBox.java:85] [AWT-EventQueue-0]  Loading Pabies1.0-all-cds.fna
INFO [2018-01-17 22:59:33,873]  [GenomeComboBox.java:96] [pool-2-thread-2]  Loading /Volumes/mac-3/home/to_be_backupped_unsensitive/Projects/igv_test_case/Pabies1.0-all-cds.fna
INFO [2018-01-17 22:59:34,011]  [GenomeManager.java:182] [pool-2-thread-2]  Loading genome: /Volumes/mac-3/home/to_be_backupped_unsensitive/Projects/igv_test_case/Pabies1.0-all-cds.fna
INFO [2018-01-17 22:59:34,864]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2018-01-17 22:59:36,235]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2018-01-17 22:59:36,322]  [GenomeManager.java:271] [pool-2-thread-2]  Genome loaded.  id= /Volumes/mac-3/home/to_be_backupped_unsensitive/Projects/igv_test_case/Pabies1.0-all-cds.fna
INFO [2018-01-17 22:59:53,700]  [IGV.java:1383] [pool-2-thread-3]  Loading 1 resources.
INFO [2018-01-17 22:59:53,703]  [TrackLoader.java:126] [pool-2-thread-3]  Loading resource, path /Volumes/mac-3/home/to_be_backupped_unsensitive/Projects/igv_test_case/Pabies1.0-all-cds.1pc.bam
ERROR [2018-01-17 22:59:54,274]  [BAMReader.java:172] [pool-1-thread-3]  Error querying for sequence: MA_9553451g0010
java.lang.IllegalArgumentException: Invalid reference index -1
	at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
	at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
	at org.broad.igv.sam.reader.BAMReader.query(BAMReader.java:169)
	at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:161)
	at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:351)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:295)
	at org.broad.igv.sam.CoverageTrack.load(CoverageTrack.java:184)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:225)
	at org.broad.igv.ui.panel.DataPanel$$Lambda$47/1847216415.run(Unknown Source)
	at java.util.concurrent.CompletableFuture$AsyncRun.exec(CompletableFuture.java:454)
	at java.util.concurrent.CompletableFuture$Async.run(CompletableFuture.java:428)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2018-01-17 22:59:57,842]  [BAMReader.java:172] [pool-1-thread-1]  Error querying for sequence: MA_934111g0010
java.lang.IllegalArgumentException: Invalid reference index -1
	at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
	at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
	at org.broad.igv.sam.reader.BAMReader.query(BAMReader.java:169)
	at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:161)
	at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:351)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:295)
	at org.broad.igv.sam.CoverageTrack.load(CoverageTrack.java:184)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:225)
	at org.broad.igv.ui.panel.DataPanel$$Lambda$47/1847216415.run(Unknown Source)
	at java.util.concurrent.CompletableFuture$AsyncRun.exec(CompletableFuture.java:454)
	at java.util.concurrent.CompletableFuture$Async.run(CompletableFuture.java:428)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2018-01-17 22:59:57,878]  [BAMReader.java:172] [pool-1-thread-2]  Error querying for sequence: MA_934111g0010
java.lang.IllegalArgumentException: Invalid reference index -1
	at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
	at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
	at org.broad.igv.sam.reader.BAMReader.query(BAMReader.java:169)
	at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:161)
	at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:351)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:295)
	at org.broad.igv.sam.AlignmentTrack.load(AlignmentTrack.java:426)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:225)
	at org.broad.igv.ui.panel.DataPanel$$Lambda$47/1847216415.run(Unknown Source)
	at java.util.concurrent.CompletableFuture$AsyncRun.exec(CompletableFuture.java:454)
	at java.util.concurrent.CompletableFuture$Async.run(CompletableFuture.java:428)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2018-01-17 23:00:02,451]  [BAMReader.java:172] [pool-1-thread-3]  Error querying for sequence: MA_10027g0010
java.lang.IllegalArgumentException: Invalid reference index -1
	at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
	at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
	at org.broad.igv.sam.reader.BAMReader.query(BAMReader.java:169)
	at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:161)
	at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:351)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:295)
	at org.broad.igv.sam.CoverageTrack.load(CoverageTrack.java:184)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:225)
	at org.broad.igv.ui.panel.DataPanel$$Lambda$47/1847216415.run(Unknown Source)
	at java.util.concurrent.CompletableFuture$AsyncRun.exec(CompletableFuture.java:454)
	at java.util.concurrent.CompletableFuture$Async.run(CompletableFuture.java:428)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2018-01-17 23:00:02,466]  [DataPanel.java:252] [pool-1-thread-3]  Error: 
java.util.concurrent.CompletionException: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
	at java.util.concurrent.CompletableFuture.internalComplete(CompletableFuture.java:205)
	at java.util.concurrent.CompletableFuture$AsyncRun.exec(CompletableFuture.java:459)
	at java.util.concurrent.CompletableFuture$Async.run(CompletableFuture.java:428)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
	at java.util.ArrayList.rangeCheck(ArrayList.java:653)
	at java.util.ArrayList.remove(ArrayList.java:492)
	at java.util.Collections$SynchronizedList.remove(Collections.java:2426)
	at org.broad.igv.sam.AlignmentDataManager.trimCache(AlignmentDataManager.java:333)
	at org.broad.igv.sam.AlignmentDataManager.load(AlignmentDataManager.java:297)
	at org.broad.igv.sam.CoverageTrack.load(CoverageTrack.java:184)
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:225)
	at org.broad.igv.ui.panel.DataPanel$$Lambda$47/1847216415.run(Unknown Source)
	at java.util.concurrent.CompletableFuture$AsyncRun.exec(CompletableFuture.java:454)
	... 4 more

Further observations:

If I then try to load another file, then igv does nothing and remains on the blue ball.
I can reset everything by sending a SIGKILL to igv and starting igv from scratch.
if I navigate to the problem contig first, then it loads ok, but after a few navigations it tends to stop working

The text was updated successfully, but these errors were encountered:

jrobinso · 2018-01-16T21:31:54Z

Thanks for the test case. I will try to reproduce ASAP.

jrobinso · 2018-01-17T21:29:52Z

Could you elaborate on what you mean by "first contig, second, etc"? I loaded the bam and hit the first 3 in the list from the pulldown menu. They all had a single read, and no issues. Then I hit a number of others at random. Same result, single read and no issues.

I might be able to address the problem from the stack trace you provided but would like to reproduce it if possible. Should I expect different coverage (more than 1 read per contig)?

winni2k · 2018-01-17T22:03:08Z

This bam is just a bunch of contigs mapped back to themselves, so you should expect 1 read per contig.

The issue does not always happen on the third contig (MA_10027g0010). Sometimes I have to navigate to a few more before returning to the third contig before the error happens.

I have gone through the steps above again and I am updating the original post with the full igv run log.

jrobinso · 2018-01-17T23:50:45Z

I just can't get it to happen. Could you share your prefs.properties file? Its possible some non-default preference is needed to set this off. Otherwise I can work with the stack trace, try to address or protect agains those errors, then ask you to try again.

jrobinso · 2018-01-18T00:34:50Z

Studying your stacktrace, it looks like this bug could be fixed with release 2.4.6. Could you try that version and let me know? You can download it from http://software.broadinstitute.org/software/igv/download

We do not create the homebrew installation, I'm not sure where that comes from or how its updated.

winni2k · 2018-01-18T08:18:36Z

I can confirm that igv 2.4.6 appears to work on the test case data. I'll reopen this issue if I the problem persists.

winni2k mentioned this issue Jan 14, 2018

Error encountered querying alignments: java.lang.ArrayIndexOutOfBoundsException: 8517 #499

Closed

winni2k closed this as completed Jan 18, 2018

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When browsing bam file: "Error: java.util.concurrent.CompletionException: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1" #506

When browsing bam file: "Error: java.util.concurrent.CompletionException: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1" #506

winni2k commented Jan 14, 2018 •

edited

jrobinso commented Jan 16, 2018

jrobinso commented Jan 17, 2018

winni2k commented Jan 17, 2018

jrobinso commented Jan 17, 2018 •

edited

jrobinso commented Jan 18, 2018 •

edited

winni2k commented Jan 18, 2018

When browsing bam file: "Error: java.util.concurrent.CompletionException: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1" #506

When browsing bam file: "Error: java.util.concurrent.CompletionException: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1" #506

Comments

winni2k commented Jan 14, 2018 • edited

jrobinso commented Jan 16, 2018

jrobinso commented Jan 17, 2018

winni2k commented Jan 17, 2018

jrobinso commented Jan 17, 2018 • edited

jrobinso commented Jan 18, 2018 • edited

winni2k commented Jan 18, 2018

winni2k commented Jan 14, 2018 •

edited

jrobinso commented Jan 17, 2018 •

edited

jrobinso commented Jan 18, 2018 •

edited