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  • Redirecting terminal output of Bowtie

    A slightly trivial question perhaps, but does anyone know why it isn't possible to redirect the output of Bowtie to a text file? I.e. the text printed to the terminal, rather than the actual alignments?

    Here's the command, which always outputs a text file of zero size:

    bowtie -p 3 -S mm9 -1 myfile1.fastq -2 myfile2.fastq myfile.sam > myfile-Log.txt

    Many thanks,

    Adam

  • #2
    I believe that the text you want is put out on stderr not stdout. So you should be able to capture it via a redirect to stderr. E.g., in bash:

    2>myfile-log.txt

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    • #3
      BTW: I've gotten into the habit, especially since most of my commands are run on a batch queuing system, of redirecting all commands to a file so that I can examine them while they are running. E.g.,

      my_command_that_is_sent_to_the_queue 2>&1 | tee my_command.stdout.stderr.txt

      This probably does not apply to you but I wanted to mention it in case someone could use the idea.

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      • #4
        This worked a treat, thanks Rick!

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