PR 910 introduces regression whereby sorting collection throws exceptions at JVM exit

[tfenne]

@magicDGS It looks to me like your PR #910 changes the behavior of temporary file creation and cleanup in a way that breaks lots of downstream usage.

The problem appears to be in DeletePathThread where it attempts to delete a Path and rethrows any exceptions that are encountered. The problem is that one of those exceptions that can be thrown is a NoSuchFileException because the file has already been cleaned up.

Running SortSam using the latest version of Picard I get:

$  java -Xmx4g -jar picard.jar SortSam I=in.bam O=out.bam SO=queryname
...
INFO	2017-11-16 07:50:23	SortSam	Finished reading inputs, merging and writing to output now.
[Thu Nov 16 07:50:27 EST 2017] picard.sam.SortSam done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=1586495488
Exception in thread "Thread-2" Exception in thread "Thread-1" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/mz/34h8j89n1jj2mg6frd0lmqxh0000gn/T/tfenne/sortingcollection.3170510762910173658.tmp
	at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
Caused by: java.nio.file.NoSuchFileException: /var/folders/mz/34h8j89n1jj2mg6frd0lmqxh0000gn/T/tfenne/sortingcollection.3170510762910173658.tmp
	at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
	at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
	at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
	at java.nio.file.Files.delete(Files.java:1126)
	at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/mz/34h8j89n1jj2mg6frd0lmqxh0000gn/T/tfenne/sortingcollection.5241745018661624118.tmp
	at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
Caused by: java.nio.file.NoSuchFileException: /var/folders/mz/34h8j89n1jj2mg6frd0lmqxh0000gn/T/tfenne/sortingcollection.5241745018661624118.tmp
	at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
	at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
	at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
	at java.nio.file.Files.delete(Files.java:1126)
	at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)

This is happening, I believe, because SortingCollection has already cleaned up it's temporary files on close, and the belt-and-suspenders of deleting on exit fails because the files are no longer there.

[magicDGS]

I guess that this can be solved using Files.deleteIfExists in DeletePathThread instead of the current implementation, to do not throw in such a case.

I can't do a PR until next week, so if it's urgent I'll recommend to submit it by yourself. Sorry for the inconvenience...

[yfarjoun]

This also implies that the SortSam isn't tested in a way that forces files to be written to disk...hmmm.

[tfenne]

@yfarjoun I don't think that's right. I think it's that SortSam isn't tested in a way that the JVM it's running in exits such that it triggers the JVM shutdown hooks that run this code.

[yfarjoun]

ah... good point.

[tbl3rd]

@tfenne @yfarjoun What Tim said. The SortingCollectionTest reliably succeeds, but then the test runner throws like crazy when shutting down.

htsjdk.samtools.util.RuntimeIOException:
  java.nio.file.NoSuchFileException:
    /var/folders/yk/9xqbctq514x_46wjqyh6294jt97pxd/T/tbl/SortingCollectionTest/sortingcollection.8451775603646045897.tmp
	at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
Caused by: java.nio.file.NoSuchFileException:
  /var/folders/yk/9xqbctq514x_46wjqyh6294jt97pxd/T/tbl/SortingCollectionTest/sortingcollection.8451775603646045897.tmp
	at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
	at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
	at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
	at java.nio.file.Files.delete(Files.java:1126)
	at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)