Picard cannot write to stdout

[nh13]

It looks like it is checking the output for a termination block, but the output is a pipe, so it should never get to BlockCompressedOutputStream.java:286. The command I am using is below.

java -jar build/libs/picard.jar FastqToSam F1=./testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq O=/dev/stdout SAMPLE_NAME=Name > out.bam
[Tue Aug 16 22:46:27 EDT 2016] picard.sam.FastqToSam FASTQ=./testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq OUTPUT=/dev/stdout SAMPLE_NAME=Name    USE_SEQUENTIAL_FASTQS=false READ_GROUP_NAME=A SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 22:46:27 EDT 2016] Executing as nhomer@Nils on Mac OS X 10.11.2 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_66-b17; Picard version: 2.6.0-7-gd4350fc-SNAPSHOT
INFO    2016-08-16 22:46:27 FastqToSam  Auto-detected quality format as: Standard.
INFO    2016-08-16 22:46:27 FastqToSam  Processed 4952 fastq reads
[Tue Aug 16 22:46:27 EDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=257425408
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" 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

Related to fulcrumgenomics/fgbio#64

[nh13]

As another datapoint, I have another tool that has the same problem.

[nh13]

samtools/htsjdk#901