net.sf.samtools.util.RuntimeIOException: File not found:

Unix & Linux | biorunner88 | 10 months ago
  1. 0

    Program just works in one terminal

    Stack Overflow | 10 months ago | biorunner88
    net.sf.samtools.util.RuntimeIOException: File not found:
  2. 0

    Program just works in one terminal

    Unix & Linux | 10 months ago | biorunner88
    net.sf.samtools.util.RuntimeIOException: File not found:
  3. 0

    Trying to Run CAP Example with standalone configuration

    Google Groups | 2 years ago | nitin tonk
    java.io.FileNotFoundException: (No such file or directory)
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  5. 0

    GitHub comment 30#3016563

    GitHub | 5 years ago | jburel
    java.io.FileNotFoundException: (No such file or directory)

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Root Cause Analysis

  1. java.io.FileNotFoundException

    (No such file or directory)

    at java.io.FileOutputStream.open()
  2. Java RT
    FileOutputStream.<init>
    1. java.io.FileOutputStream.open(Native Method)
    2. java.io.FileOutputStream.<init>(FileOutputStream.java:221)
    3. java.io.FileOutputStream.<init>(FileOutputStream.java:171)
    3 frames
  3. picard
    ReorderSam.main
    1. net.sf.samtools.util.BinaryCodec.<init>(BinaryCodec.java:95)
    2. net.sf.samtools.util.BlockCompressedOutputStream.<init>(BlockCompressedOutputStream.java:127)
    3. net.sf.samtools.BAMFileWriter.<init>(BAMFileWriter.java:50)
    4. net.sf.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:154)
    5. net.sf.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:136)
    6. net.sf.samtools.SAMFileWriterFactory.makeSAMOrBAMWriter(SAMFileWriterFactory.java:246)
    7. net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:118)
    8. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
    9. net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:120)
    10. net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
    10 frames