htsjdk.samtools.util.RuntimeIOException

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    • htsjdk.samtools.util.RuntimeIOException: /dev/stdout (Permission denied) at htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:610) at htsjdk.samtools.BAMFileWriter.finish(BAMFileWriter.java:143) at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:219) at picard.sam.FastqToSam.doWork(FastqToSam.java:290) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105) Caused by: java.io.FileNotFoundException: /dev/stdout (Permission denied) at java.io.RandomAccessFile.open0(Native Method) at java.io.RandomAccessFile.open(RandomAccessFile.java:316) at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243) at htsjdk.samtools.util.BlockCompressedInputStream.checkTermination(BlockCompressedInputStream.java:471) at htsjdk.samtools.util.BlockCompressedOutputStream.close(BlockCompressedOutputStream.java:286) at java.io.FilterOutputStream.close(FilterOutputStream.java:159) at htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:606) ... 6 more

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