igv_2.3.3.1 error with a specific load
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Anne Deslattes Mays
Mar 20, 2014, 10:35:09 AM3/20/14
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Hello,
Here is the log. Consistently on just this single location of approximate 1500 bp.
I have 4 experiments I have mapped to a transcriptome via bowtie2, creating bam files for each of them.
Stepping through each of the abundant transcripts, I got an error with the largest bam file but not on the most abundant transcript.
Here is the log. Consistently on just this single location of approximate 1500 bp.
I am running on a Mac Book Pro. 8GB. OS X 10.9.2.
INFO [2014-03-20 10:28:40,350] [TrackLoader.java:112] Loading resource, path /Users/adeslat/Desktop/newcode/code/Georgetown/boneMarrowRNASeq/alignments/illumina.total.bm.bt2.pacbio.good.collapsed.sorted.bam
ERROR [2014-03-20 10:28:40,464] [AlignmentTileLoader.java:237] Error loading alignment data
java.lang.RuntimeException: Invalid file pointer: 1385822722816799
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:549)
at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:648)
at net.sf.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:598)
at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:352)
at net.sf.samtools.SAMFileReader.query(SAMFileReader.java:373)
at org.broad.igv.sam.reader.BAMFileReader.query(BAMFileReader.java:98)
at org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:123)
at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:389)
at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:354)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Caused by: java.io.IOException: Invalid file pointer: 1385822722816799
at net.sf.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:283)
at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:661)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:532)
... 13 more
INFO [2014-03-20 10:28:40,465] [MessageUtils.java:60] <html>Error encountered querying alignments: java.lang.RuntimeException: Invalid file pointer: 1385822722816799
INFO [2014-03-20 10:28:45,985] [MessageUtils.java:60] <html>Unexpected error: null.<br>See igv.log for more details
ERROR [2014-03-20 10:28:47,465] [LongRunningTask.java:60] Exception running task
java.lang.NullPointerException
at org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:392)
at org.broad.igv.sam.AlignmentDataManager$1.run(AlignmentDataManager.java:354)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Jim Robinson
Mar 20, 2014, 10:53:00 AM3/20/14
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Hi,
This looks like a problem with the BAM file, or perhaps the index. Have you tried viewing the same location with samtools?
Jim
This looks like a problem with the BAM file, or perhaps the index. Have you tried viewing the same location with samtools?
Jim
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Anne Deslattes Mays
Mar 20, 2014, 11:47:55 AM3/20/14
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Hi Jim,
Thanks — you are right — I only transferred half of the file — bam file was truncated.
Best,
Anne
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