Hey Josephw,
we are tracking your issue here:
https://github.com/broadinstitute/picard/issues/137
N
On Tue, Dec 2, 2014 at 12:09 AM, Qingguo Wang <josephw10...@gmail.com>
wrote:
>
> 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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