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

GitHub | nh13 | 6 months ago
tip
Your exception is missing from the Samebug knowledge base.
Here are the best solutions we found on the Internet.
Click on the to mark the helpful solution and get rewards for you help.
  1. 0

    Picard cannot write to stdout

    GitHub | 6 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 | 7 months ago | tfenne
    htsjdk.samtools.util.RuntimeIOException: /dev/stdout (Permission denied)
  3. 0

    GitHub comment 64#233807329

    GitHub | 7 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

    GitHub comment 952#145085983

    GitHub | 1 year ago | hlship
    java.lang.Error: java.lang.reflect.InvocationTargetException
  6. 0

    ImageJ plugin import remote with https

    GitHub | 2 years ago | dpwrussell
    java.io.FileNotFoundException: https:/s3.amazonaws.com/dpwr/s3test/bus.png (No such file or directory)

  1. Mark 1 times, last 1 month ago
  2. andyglick 3 times, last 1 month ago
  3. johnxfly 4 times, last 2 months ago
  4. Andreas Häber 1 times, last 3 months ago
  5. tyson925 5 times, last 9 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