Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

    Comment


    • #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

      Comment


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

        Comment


        • #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.

          Comment


          • #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.

            Comment


            • #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.

              Comment


              • #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.

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Strategies for Sequencing Challenging Samples
                  by seqadmin


                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                  03-22-2024, 06:39 AM
                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 03-27-2024, 06:37 PM
                0 responses
                13 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-27-2024, 06:07 PM
                0 responses
                12 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-22-2024, 10:03 AM
                0 responses
                53 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-21-2024, 07:32 AM
                0 responses
                69 views
                0 likes
                Last Post seqadmin  
                Working...
                X