The bam file I tested is a RNA-seq sample. The following is the error
message from RevertBam. Any clue to fix it?
Thanks in advance,
Josephw
......
INFO 2014-12-01 16:39:03 RevertSam Reverted 165,000,000 records. Elapsed
time: 00:46:06s. Time for last 1,000,000: 1s. Last read position: */*
INFO 2014-12-01 16:39:17 RevertSam Reverted 166,000,000 records. Elapsed
time: 00:46:20s. Time for last 1,000,000: 13s. Last read position: */*
[Mon Dec 01 16:40:29 EST 2014] picard.sam.RevertSam done. Elapsed time:
47.54 minutes.
Runtime.totalMemory()=12187664384
To get help, see
http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.util.NoSuchElementException
at
htsjdk.samtools.util.SortingCollection$FileRecordIterator.next(SortingCollection.java:472)
at htsjdk.samtools.util.PeekIterator.peek(PeekIterator.java:67)
at
htsjdk.samtools.util.SortingCollection$PeekFileRecordIteratorComparator.compare(SortingCollection.java:507)
at
htsjdk.samtools.util.SortingCollection$PeekFileRecordIteratorComparator.compare(SortingCollection.java:504)
at java.util.TreeMap.getEntryUsingComparator(TreeMap.java:368)
at java.util.TreeMap.getEntry(TreeMap.java:339)
at java.util.TreeMap.remove(TreeMap.java:597)
at java.util.TreeSet.remove(TreeSet.java:276)
at
htsjdk.samtools.util.SortingCollection$PollableTreeSet.poll(SortingCollection.java:525)
at
htsjdk.samtools.util.SortingCollection$MergingIterator.next(SortingCollection.java:420)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:199)
at picard.sam.RevertSam.doWork(RevertSam.java:230)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
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