stdin/stdout error while pipe

[xiucz]

Hi,

When I use the following command to check fastqs, however it returns the error. But without using pipe into fastp, it works well.

May I get your opinion on this?

fastp version[0.23.0]

gatk SamToFastq \
--CLIPPING_ATTRIBUTE XT  --CLIPPING_ACTION 2 \
--FASTQ /dev/stdout --INTERLEAVE true -NON_PF true \
--TMP_DIR -I umi.ubam |  \
fastp --stdin --interleaved_in  \
--html my.html --json my.json -o fq1.gz -O fq2.gz

And here is the error log:

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMException: Error in writing fastq file /dev/stdout
        at htsjdk.samtools.fastq.BasicFastqWriter.checkError(BasicFastqWriter.java:69)
        at htsjdk.samtools.fastq.BasicFastqWriter.flush(BasicFastqWriter.java:75)
        at htsjdk.samtools.fastq.BasicFastqWriter.close(BasicFastqWriter.java:81)
        at htsjdk.samtools.fastq.AsyncFastqWriter.synchronouslyClose(AsyncFastqWriter.java:19)
        at htsjdk.samtools.util.AbstractAsyncWriter.close(AbstractAsyncWriter.java:89)
        at picard.sam.SamToFastq$FastqWriters.closeAll(SamToFastq.java:541)
        at picard.sam.SamToFastq$FastqWriters.access$000(SamToFastq.java:500)
        at picard.sam.SamToFastq.doWork(SamToFastq.java:214)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
        at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)
Segmentation fault

Best, xiucz