Merged BAM File error (java.lang.IllegalStateException: Iteration in progress)

Kei Saito

unread,

Jun 9, 2011, 1:28:31 AM6/9/11

to igv-help

Hello,

An error occured when I opened and operated Merged BAM File
(.bam.list) with IGV 2.0.
Below is the operation leading to the error.
1) displaying some reads.
2) reloading alignment data. (e.g. jumps to reads in another
chromosome)

Any idea why this happens?

Thanks,
Kei

OS: Windows 7 Professional 64bit
Java version:
c:\>java -version
java version "1.6.0_25"
Java(TM) SE Runtime Environment (build 1.6.0_25-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.0-b11, mixed mode)
Error log:
--------------------------------------------------------------------------------
ERROR [2011-06-06 13:53:49,256] [CachingQueryReader.java:341] [pool-3-
thread-2] Error loading alignment data
java.lang.IllegalStateException: Iteration in progress
at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:263)
at net.sf.samtools.SAMFileReader.query(SAMFileReader.java:329)
at org.broad.igv.sam.reader.BAMQueryReader.query(BAMQueryReader.java:
95)
at org.broad.igv.sam.reader.MergedAlignmentReader
$MergedFileIterator.<init>(MergedAlignmentReader.java:99)
at
org.broad.igv.sam.reader.MergedAlignmentReader.query(MergedAlignmentReader.java:
53)
at
org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:
228)
at
org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:
183)
at org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:
123)
at org.broad.igv.sam.AlignmentDataManager
$2.run(AlignmentDataManager.java:331)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:75)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown
Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
ERROR [2011-06-06 13:53:49,258] [AlignmentDataManager.java:356]
[pool-3-thread-2] Error loading alignments
org.broad.igv.exceptions.DataLoadException: <html>An error occurred
while loading: Error: java.lang.IllegalStateException: Iteration in
progress<br>
at
org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:
342)
at
org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:
183)
at org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:
123)
at org.broad.igv.sam.AlignmentDataManager
$2.run(AlignmentDataManager.java:331)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:75)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown
Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

James Robinson

unread,

Jun 9, 2011, 9:15:40 PM6/9/11

to igv-...@googlegroups.com

Hi Kei,

This appears to be a threading issue. I am working on a solution now and will update you when it is available.

regards,

Jim

Jim Robinson

unread,

Jun 9, 2011, 10:35:42 PM6/9/11

to igv-help

Hi Kei,

Thank you for reporting this. I have identified the cause and applied
a fix to the early access IGV, available from here

http://www.broadinstitute.org/software/igv/download_dev

This fix will be released tommorrow in a Version 2.0 update, along
with other bug fixes.

regards,

Jim

Kei Saito

unread,

Jun 10, 2011, 4:43:54 AM6/10/11

to igv-help

Hi Jim,

Thanks for your prompt response!
I have confirmed that the error does not occur in the early access
IGV.

Thanks,
Kei

Reply all

Reply to author

Forward