INFO [2011-01-17 09:39:44,696] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-17 09:39:45,067] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-17 09:39:45,408] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-17 09:39:47,402] [GenomeManager.java:118] [SwingWorker-pool-948129019-thread-1] Genome loaded INFO [2011-01-17 09:40:30,579] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-17 09:40:57,247] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-17 09:42:20,657] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. ERROR [2011-01-17 09:42:20,853] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:20,853] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:23,599] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:23,600] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:24,851] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:24,852] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:25,885] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:25,886] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:43,779] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:43,780] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:46,412] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:46,413] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:48,486] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:48,486] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:50,586] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:50,586] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:51,365] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:42:51,365] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:43:01,656] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-17 09:43:04,128] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-17 09:43:04,359] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-17 09:43:04,593] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-17 09:43:15,403] [GenomeManager.java:118] [SwingWorker-pool-920911839-thread-1] Genome loaded INFO [2011-01-17 09:43:36,068] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-17 09:43:42,591] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-17 09:44:45,285] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. ERROR [2011-01-17 09:45:30,678] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:30,678] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:30,679] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:30,680] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:35,349] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:35,349] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:35,350] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:35,350] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:36,504] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:36,504] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:36,504] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:36,505] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:37,776] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:37,776] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:37,777] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:37,777] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:39,909] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:39,910] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 25
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:39,910] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-17 09:45:39,911] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -94
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:45:45,905] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-17 09:45:49,855] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-17 09:45:50,053] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-17 09:45:50,282] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-17 09:46:00,851] [GenomeManager.java:118] [SwingWorker-pool-1505607660-thread-1] Genome loaded INFO [2011-01-17 09:46:26,126] [SessionReader.java:739] [SwingWorker-pool-1505607660-thread-3] Warning. No tracks were found with id: Reference in session file INFO [2011-01-17 09:46:44,318] [GenomeManager.java:408] [SwingWorker-pool-1505607660-thread-4] Refreshing genome: http://igvdata.broadinstitute.org/genomes/hg18.genome INFO [2011-01-17 09:46:58,688] [GenomeManager.java:408] [SwingWorker-pool-1505607660-thread-5] Refreshing genome: http://igvdata.broadinstitute.org/genomes/hg17.genome INFO [2011-01-17 09:47:17,413] [GenomeManager.java:408] [SwingWorker-pool-1505607660-thread-6] Refreshing genome: http://igvdata.broadinstitute.org/genomes/tair10.genome ERROR [2011-01-17 09:48:20,454] [GenomeManager.java:422] [SwingWorker-pool-1505607660-thread-4] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:411) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:257) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:244) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:48:23,873] [GenomeManager.java:118] [SwingWorker-pool-1505607660-thread-4] Genome loaded ERROR [2011-01-17 09:48:31,562] [GenomeManager.java:422] [SwingWorker-pool-1505607660-thread-5] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:411) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:257) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:244) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:48:33,493] [GenomeManager.java:118] [SwingWorker-pool-1505607660-thread-5] Genome loaded INFO [2011-01-17 09:48:33,896] [SequenceManager.java:348] [pool-1-thread-1] Converting sequence URL: http://www.broad.mit.edu/igv/SequenceServlet/hg17 -> http://www.broadinstitute.org/igvdata/annotations/seq/hg17 INFO [2011-01-17 09:48:37,621] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-17 09:48:42,226] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-17 09:48:42,374] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-17 09:48:42,615] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-17 09:48:48,906] [GenomeManager.java:408] [SwingWorker-pool-1358669058-thread-1] Refreshing genome: http://igvdata.broadinstitute.org/genomes/hg17.genome ERROR [2011-01-17 09:51:06,511] [GenomeManager.java:422] [SwingWorker-pool-1358669058-thread-1] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:411) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.findGenomeAndLoad(GenomeManager.java:224) at org.broad.igv.session.ViewContext.setGenomeId(ViewContext.java:726) at org.broad.igv.ui.IGVMainFrame.setGenomeId(IGVMainFrame.java:1833) at org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java:2698) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:51:09,612] [GenomeManager.java:118] [SwingWorker-pool-1358669058-thread-1] Genome loaded INFO [2011-01-17 09:51:25,947] [GenomeManager.java:408] [SwingWorker-pool-1358669058-thread-4] Refreshing genome: http://igvdata.broadinstitute.org/genomes/tair10.genome ERROR [2011-01-17 09:54:09,498] [GenomeManager.java:422] [SwingWorker-pool-1358669058-thread-3] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:418) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:257) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:244) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) WARN [2011-01-17 09:54:14,992] [GenomeManager.java:187] [SwingWorker-pool-1358669058-thread-3] Error loading genome archive: /home/xianggan/igv/genomes/mm8.genome java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(ZipFile.java:114) at java.util.zip.ZipFile.(ZipFile.java:75) at org.broad.igv.feature.GenomeManager.createGenomeDescriptor(GenomeManager.java:455) at org.broad.igv.feature.GenomeManager.loadGenomeFromLocalFile(GenomeManager.java:176) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:367) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:257) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:244) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:54:14,993] [GenomeManager.java:408] [SwingWorker-pool-1358669058-thread-3] Refreshing genome: http://igvdata.broadinstitute.org/genomes/hg18.genome ERROR [2011-01-17 09:54:50,550] [GenomeManager.java:422] [SwingWorker-pool-1358669058-thread-4] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:411) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:257) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:244) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:54:53,639] [GenomeManager.java:118] [SwingWorker-pool-1358669058-thread-4] Genome loaded ERROR [2011-01-17 09:56:18,803] [GenomeManager.java:422] [SwingWorker-pool-1358669058-thread-3] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:411) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.findGenomeAndLoad(GenomeManager.java:224) at org.broad.igv.session.ViewContext.setGenomeId(ViewContext.java:726) at org.broad.igv.ui.IGVMainFrame.setGenomeId(IGVMainFrame.java:1833) at org.broad.igv.ui.IGVMainFrame.doChooseGenome(IGVMainFrame.java:1500) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:252) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 09:56:39,576] [GenomeManager.java:118] [SwingWorker-pool-1358669058-thread-6] Genome loaded INFO [2011-01-17 09:56:40,294] [LRUCache.java:69] [pool-1-thread-2] Memory low. Free cache entry INFO [2011-01-17 09:56:41,457] [SessionReader.java:739] [SwingWorker-pool-1358669058-thread-5] Warning. No tracks were found with id: Reference in session file INFO [2011-01-17 09:56:53,667] [GenomeManager.java:408] [SwingWorker-pool-1358669058-thread-7] Refreshing genome: http://igv.broadinstitute.org/genomes/b37.genome ERROR [2011-01-17 10:08:25,474] [GenomeManager.java:422] [SwingWorker-pool-1358669058-thread-7] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:411) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:257) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:244) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 10:08:27,799] [GenomeManager.java:118] [SwingWorker-pool-1358669058-thread-7] Genome loaded INFO [2011-01-17 10:09:42,334] [GenomeManager.java:408] [SwingWorker-pool-1358669058-thread-9] Refreshing genome: http://igvdata.broadinstitute.org/genomes/tair9.genome ERROR [2011-01-17 10:13:07,658] [GenomeManager.java:422] [SwingWorker-pool-1358669058-thread-9] Error refreshing genome cache. java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.read1(BufferedInputStream.java:256) at java.io.BufferedInputStream.read(BufferedInputStream.java:317) at sun.net.www.MeteredStream.read(MeteredStream.java:116) at java.io.FilterInputStream.read(FilterInputStream.java:116) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2669) at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2664) at org.broad.igv.util.FileUtils.createFileFromStream(FileUtils.java:356) at org.broad.igv.feature.GenomeManager.refreshCache(GenomeManager.java:411) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:316) at org.broad.igv.feature.GenomeManager.loadGenome(GenomeManager.java:257) at org.broad.igv.ui.IGVCommandBar$2$2.doInBackground(IGVCommandBar.java:244) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-17 10:13:33,681] [GenomeManager.java:118] [SwingWorker-pool-1358669058-thread-9] Genome loaded INFO [2011-01-17 10:27:10,979] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-18 16:51:42,714] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-18 16:51:44,144] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-18 16:51:45,043] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-18 16:51:50,431] [GenomeManager.java:408] [SwingWorker-pool-839033548-thread-1] Refreshing genome: http://igv.broadinstitute.org/genomes/b37.genome INFO [2011-01-18 16:52:21,857] [GenomeManager.java:118] [SwingWorker-pool-839033548-thread-1] Genome loaded INFO [2011-01-18 17:00:22,063] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-18 17:02:29,276] [GenomeManager.java:408] [SwingWorker-pool-839033548-thread-3] Refreshing genome: http://igvdata.broadinstitute.org/genomes/tair10.genome INFO [2011-01-18 17:02:35,562] [GenomeManager.java:118] [SwingWorker-pool-839033548-thread-3] Genome loaded INFO [2011-01-18 17:02:52,076] [LRUCache.java:69] [pool-1-thread-1] Memory low. Free cache entry INFO [2011-01-18 17:03:29,770] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. ERROR [2011-01-18 17:03:29,977] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:29,978] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:44,390] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:44,391] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:48,419] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:48,420] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:49,471] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:49,472] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:50,489] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:03:50,490] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:04:05,521] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:04:05,522] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:04:06,716] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:04:06,717] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:04:10,113] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:04:10,114] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-18 17:04:28,322] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-18 17:04:34,228] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-18 17:04:34,789] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-18 17:04:36,926] [GenomeManager.java:118] [SwingWorker-pool-1892658481-thread-1] Genome loaded INFO [2011-01-18 17:05:07,734] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-18 17:05:57,212] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-18 17:05:57,391] [LRUCache.java:69] [pool-1-thread-3] Memory low. Free cache entry ERROR [2011-01-18 17:05:58,276] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:05:58,277] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:06:13,407] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:06:13,408] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:06:14,457] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:06:14,458] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:06:15,483] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28 at net.sf.samtools.SAMUtils.compressedBaseToByteLow(SAMUtils.java:175) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:86) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:06:15,485] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: 28
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-18 17:06:22,713] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-18 17:06:26,347] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-18 17:06:26,497] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-18 17:06:26,800] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-18 17:06:28,307] [GenomeManager.java:118] [SwingWorker-pool-960389670-thread-1] Genome loaded INFO [2011-01-18 17:06:52,158] [SessionReader.java:739] [SwingWorker-pool-960389670-thread-3] Warning. No tracks were found with id: Genes in session file INFO [2011-01-18 17:23:58,119] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-18 17:23:58,271] [LRUCache.java:69] [pool-1-thread-1] Memory low. Free cache entry ERROR [2011-01-18 17:23:59,831] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:23:59,832] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:08,119] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:08,120] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:09,279] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:09,280] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:11,524] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:11,525] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:16,338] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:24:16,339] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-18 17:24:26,085] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-18 17:25:25,438] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-18 17:25:25,683] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-18 17:25:26,192] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-18 17:25:28,774] [GenomeManager.java:118] [SwingWorker-pool-1520159108-thread-1] Genome loaded INFO [2011-01-18 17:25:51,950] [SessionReader.java:739] [SwingWorker-pool-1520159108-thread-3] Warning. No tracks were found with id: Genes in session file INFO [2011-01-18 17:33:51,316] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-18 17:35:54,741] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-18 17:41:14,514] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-18 17:41:14,811] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-18 17:41:15,387] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-18 17:41:17,523] [GenomeManager.java:118] [SwingWorker-pool-1485335248-thread-1] Genome loaded INFO [2011-01-18 17:41:37,801] [SessionReader.java:739] [SwingWorker-pool-1485335248-thread-3] Warning. No tracks were found with id: Genes in session file INFO [2011-01-18 17:41:48,762] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. ERROR [2011-01-18 17:41:48,933] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:41:48,934] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:41:51,054] [CachingQueryReader.java:253] [pool-1-thread-2] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:41:51,055] [AlignmentDataManager.java:220] [pool-1-thread-2] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:41:56,946] [CachingQueryReader.java:253] [pool-1-thread-3] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:41:56,947] [AlignmentDataManager.java:220] [pool-1-thread-3] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:41:58,849] [CachingQueryReader.java:253] [pool-1-thread-1] Error loading alignment data java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63 at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199) at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85) at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:335) at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:264) at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:192) at org.broad.igv.sam.SamAlignment.(SamAlignment.java:111) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:212) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) ERROR [2011-01-18 17:41:58,850] [AlignmentDataManager.java:220] [pool-1-thread-1] Error loading alignments org.broad.igv.exceptions.DataLoadException: An error occurred while loading: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -63
at org.broad.igv.sam.reader.CachingQueryReader.loadTiles(CachingQueryReader.java:254) at org.broad.igv.sam.reader.CachingQueryReader.getTiles(CachingQueryReader.java:171) at org.broad.igv.sam.reader.CachingQueryReader.query(CachingQueryReader.java:112) at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:201) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:71) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) INFO [2011-01-18 17:42:03,534] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-01-26 13:08:11,253] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-01-26 13:08:12,456] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-01-26 13:08:13,155] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-01-26 13:08:15,482] [GenomeManager.java:408] [SwingWorker-pool-809420129-thread-1] Refreshing genome: http://igvdata.broadinstitute.org/genomes/tair10.genome INFO [2011-01-26 13:08:18,480] [GenomeManager.java:118] [SwingWorker-pool-809420129-thread-1] Genome loaded INFO [2011-01-26 13:10:45,311] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-01-26 14:57:27,613] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-05-11 09:23:04,586] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-05-11 09:24:40,960] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-05-11 09:24:41,462] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-05-11 09:24:42,125] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-05-11 09:24:44,951] [GenomeManager.java:118] [SwingWorker-pool-647098590-thread-1] Genome loaded INFO [2011-05-11 09:24:55,524] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-05-11 09:28:16,582] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-05-11 09:28:16,928] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-05-11 09:28:17,434] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-05-11 09:28:19,907] [GenomeManager.java:118] [SwingWorker-pool-1147380142-thread-1] Genome loaded INFO [2011-05-11 09:28:27,059] [ShutdownThread.java:47] [Thread-4] Closing HDF5 INFO [2011-06-06 14:30:39,630] [IGVMainFrame.java:2536] [main] IGV Version 1.5.48 (6177)01/05/2011 10:58 AM INFO [2011-06-06 14:30:40,452] [IGVMainFrame.java:2541] [main] Default User Directory: /home/xianggan INFO [2011-06-06 14:30:41,109] [CommandListener.java:64] [Thread-5] Listening on port 60151 INFO [2011-06-06 14:30:43,341] [GenomeManager.java:118] [SwingWorker-pool-647098590-thread-1] Genome loaded INFO [2011-06-06 14:31:13,228] [GenomeManager.java:118] [SwingWorker-pool-647098590-thread-2] Genome loaded INFO [2011-06-06 14:31:39,873] [GenomeManager.java:408] [SwingWorker-pool-647098590-thread-3] Refreshing genome: http://igvdata.broadinstitute.org/genomes/rn4.genome INFO [2011-06-06 14:31:40,776] [GenomeManager.java:118] [SwingWorker-pool-647098590-thread-3] Genome loaded INFO [2011-06-06 14:31:51,971] [TrackManager.java:225] [AWT-EventQueue-0] Loading1 resources. INFO [2011-06-06 16:56:16,947] [ShutdownThread.java:47] [Thread-4] Closing HDF5