htsjdk.samtools.util.RuntimeIOException: /dev/stdout (Permission denied)

GitHub | nh13 | 8 months ago
tip
Click on the to mark the solution that helps you, Samebug will learn from it.
As a community member, you’ll be rewarded for you help.
  1. 0

    Picard cannot write to stdout

    GitHub | 8 months ago | nh13
    htsjdk.samtools.util.RuntimeIOException: /dev/stdout (Permission denied)
  2. 0

    CallMolecularConsensusReads doesn't appear to support /dev/stdout as it's output file

    GitHub | 9 months ago | tfenne
    htsjdk.samtools.util.RuntimeIOException: /dev/stdout (Permission denied)
  3. 0

    GitHub comment 64#233807329

    GitHub | 9 months ago | nh13
    htsjdk.samtools.util.RuntimeIOException: /dev/stdout (Permission denied)
  4. Speed up your debug routine!

    Automated exception search integrated into your IDE

  5. 0

    Using JWNL, too many open files in system

    Stack Overflow | 12 months ago | hao
    net.didion.jwnl.JWNLException: Unable to install net.didion.jwnl.dictionary.FileBackedDictionary
  6. 0

    GitHub comment 952#145085983

    GitHub | 2 years ago | hlship
    java.lang.Error: java.lang.reflect.InvocationTargetException

  1. johnxfly 4 times, last 2 weeks ago
  2. Mark 1 times, last 2 months ago
  3. andyglick 3 times, last 3 months ago
  4. Andreas Häber 1 times, last 5 months ago
  5. tyson925 5 times, last 11 months ago
1 more registered users
30 unregistered visitors
Not finding the right solution?
Take a tour to get the most out of Samebug.

Tired of useless tips?

Automated exception search integrated into your IDE

Root Cause Analysis

  1. java.io.FileNotFoundException

    /dev/stdout (Permission denied)

    at java.io.RandomAccessFile.open0()
  2. Java RT
    RandomAccessFile.<init>
    1. java.io.RandomAccessFile.open0(Native Method)
    2. java.io.RandomAccessFile.open(RandomAccessFile.java:316)
    3. java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
    3 frames
  3. HTS JDK
    BlockCompressedOutputStream.close
    1. htsjdk.samtools.util.BlockCompressedInputStream.checkTermination(BlockCompressedInputStream.java:471)
    2. htsjdk.samtools.util.BlockCompressedOutputStream.close(BlockCompressedOutputStream.java:286)
    2 frames
  4. Java RT
    FilterOutputStream.close
    1. java.io.FilterOutputStream.close(FilterOutputStream.java:159)
    1 frame
  5. HTS JDK
    SAMFileWriterImpl.close
    1. htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:606)
    2. htsjdk.samtools.BAMFileWriter.finish(BAMFileWriter.java:143)
    3. htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:219)
    3 frames
  6. picard.sam
    FastqToSam.doWork
    1. picard.sam.FastqToSam.doWork(FastqToSam.java:290)
    1 frame
  7. picard.cmdline
    PicardCommandLine.main
    1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
    2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
    3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
    3 frames