htsjdk.samtools.SAMException: Exception creating temporary directory.

GitHub | yhoogstrate | 2 years ago
  1. 0

    GitHub comment 139#105573415

    GitHub | 2 years ago | yhoogstrate
    htsjdk.samtools.SAMException: Exception creating temporary directory.
  2. 0

    Error running Picard tools (devteam)

    usegalaxy.org | 8 months ago
    htsjdk.samtools.SAMException: Exception creating temporary directory.
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    Error when docker added for Picard tools.

    GitHub | 12 months ago | FarahZKhan
    htsjdk.samtools.SAMException: Exception creating temporary directory.
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  5. 0

    Error in installation setup.log

    GitHub | 2 years ago | yurem
    java.io.IOException: Permission denied
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    WLST by Examples: WLST Issues

    blogspot.com | 1 year ago
    java.io.IOException: Permission denied

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Root Cause Analysis

  1. java.io.IOException

    Permission denied

    at java.io.UnixFileSystem.createFileExclusively()
  2. Java RT
    File.createTempFile
    1. java.io.UnixFileSystem.createFileExclusively(Native Method)
    2. java.io.File.createNewFile(File.java:1006)
    3. java.io.File.createTempFile(File.java:1989)
    4. java.io.File.createTempFile(File.java:2040)
    4 frames
  3. HTS JDK
    CoordinateSortedPairInfoMap.<init>
    1. htsjdk.samtools.util.IOUtil.createTempDir(IOUtil.java:668)
    2. htsjdk.samtools.CoordinateSortedPairInfoMap.<init>(CoordinateSortedPairInfoMap.java:59)
    2 frames
  4. picard.sam.markduplicates
    MarkDuplicates.doWork
    1. picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.<init>(DiskBasedReadEndsForMarkDuplicatesMap.java:57)
    2. picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:250)
    3. picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:114)
    3 frames
  5. picard.cmdline
    PicardCommandLine.main
    1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
    2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
    3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
    3 frames