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

GitHub | nh13 | 4 months ago
  1. 0

    Picard cannot write to stdout

    GitHub | 4 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 | 5 months ago | tfenne
    htsjdk.samtools.util.RuntimeIOException: /dev/stdout (Permission denied)
  3. 0

    GitHub comment 64#233807329

    GitHub | 5 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 | 1 year ago | dpwrussell
    java.io.FileNotFoundException: https:/s3.amazonaws.com/dpwr/s3test/bus.png (No such file or directory)

  1. Andreas Häber 1 times, last 2 weeks ago
  2. tyson925 5 times, last 7 months ago
  3. rp 13 times, last 8 months ago
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