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  • BWA in the background

    I searched for this but did not find a thread on the subject. I am trying to run BWA in the background. I tried running the command with an ampersand (&) and it didn't work. I tried the following:

    command line > output1>&output2 &

    And that didn't work. It just ends up starting the job and then stopping. I tried sending the stopped job to the background with bg and it just ended up trying to start the job and then stopping it again.

    Is there a way to run a bwa job in the background so I can close the terminal I have open to the server without it killing the job?

  • #2
    What if you put "nohup" before the command and a "&" after the command? This should let the command run in the background with all screen output directed to nohup.out

    -Jason

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    • #3
      That just stops the job as well.

      Edit:

      It looks like this is actually working so far. I will see if I get the output I desire. Thanks.
      Last edited by ercfrtz; 04-19-2011, 10:58 AM. Reason: Clarification

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      • #4
        Alternatively, try using screen. It's extremely useful for this kind of thing.

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        • #5
          watch your spaces in the command line

          Try this:

          jobwhatever > output1 2> error2 &

          Based on what I can copy/paste from your post, you are writing all output (stdout AND stderr) to one file : output2.

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          • #6
            The first & sign would only be useful if you want to write the standout and stderr to the same file:

            jobwhatever >output1 2>&1 &

            Otherwise, Richard's command will do the job.

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            • #7
              Originally posted by robs View Post
              The first & sign would only be useful if you want to write the standout and stderr to the same file:

              jobwhatever >output1 2>&1 &

              Otherwise, Richard's command will do the job.
              Please don't do this way. For bwa, stdout and stderr must be separated.

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              • #8
                The comment was meant for the general case and not particularly for BWA (that's why is says "jobwhatever").

                I agree that for BWA that is not the command you would want to use.

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