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How can I send the output of BaseRecalibrator to standard output?

PipePlumberPipePlumber Member
edited August 2012 in Ask the GATK team

Right now I am specifying the output of BaseRecalibrator with -o which sends it to disk. I'd like to send it to standard output so I can use it in my pipeline, but I can't figure out how. I tried several things:

omitting -o which gave me an error
-o - which wrote the output to a file named -
-o /dev/stdout, which failed because "##### ERROR MESSAGE: Couldn't write file /dev/stdout.csv because File /dev/stdout.csv could not be created"

How can I get this to work? It works correctly in PrintReads where omitting -o send the output to standard out.

What is /dev/stdout.csv? Are you writing temp files to the output area? Please write temp files to the temp directory and let me specify where that would go with a command line option (defaulting to /tmp).

Also, I'm seeing the log output in the standard output, even if I use -log. Please don't do this. I'd like collect the logging information, but it belongs in standard error or in the -log file, and if -log file is used, please don't send it to standard error.

Your non-human users thank you ;-)


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