Hi,
I'm starting to process a set of bams following the best practices and beginning from bams that were processed by someone else. Thus, I'm attempting to generate unmapped BAMs following this post, and using the latest version of Picard (2.15.0). Unfortunately, Picard gives an exception that shows it is unable to find temporary files it is writing. I know there's space for these files and in fact, I now have version 1.141 of Picard running without issue. The output from version 2.15.0 is below.
15:34:14.012 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/REDACTED/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Sat Nov 18 15:34:14 CST 2017] RevertSam INPUT=/REDACTED.bam OUTPUT=/REDACTED/808302_LP6008048-DNA_B02.bam SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, XT, XN, AS, OC, OP] SANITIZE=true MAX_DISCARD_FRACTION=0.005 TMP_DIR=[/REDACTED/tmp] VALIDATION_STRINGENCY=LENIENT OUTPUT_BY_READGROUP=false OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Sat Nov 18 15:34:14 CST 2017] Executing as awilliams@REDACTED on Linux 3.10.0-229.7.2.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_151-b12; Deflater: Intel; Inflater: Intel; Picard version: 2.15.0-SNAPSHOT
[Sat Nov 18 15:34:30 CST 2017] picard.sam.RevertSam done. Elapsed time: 0.27 minutes.
Runtime.totalMemory()=1272971264
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /REDACTED/tmp/awilliams/sortingcollection.728972638772980431.tmp
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:246)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:166)
at picard.sam.RevertSam$RevertSamSorter.add(RevertSam.java:637)
at picard.sam.RevertSam.doWork(RevertSam.java:260)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
Caused by: java.nio.file.NoSuchFileException: /REDACTED/tmp/awilliams/sortingcollection.728972638772980431.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.newByteChannel(UnixFileSystemProvider.java:214)
at java.nio.file.Files.newByteChannel(Files.java:361)
at java.nio.file.Files.createFile(Files.java:632)
at java.nio.file.TempFileHelper.create(TempFileHelper.java:138)
at java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:161)
at java.nio.file.Files.createTempFile(Files.java:852)
at htsjdk.samtools.util.IOUtil.newTempPath(IOUtil.java:316)
at htsjdk.samtools.util.SortingCollection.newTempFile(SortingCollection.java:255)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:220)
... 6 more
