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  • New to BAsh. Encountered an error

    This is the script which I made

    #!/bin/bash -l
    ##PBS Directives
    #PBS -q default
    #PBS -l nodes=1pn=4
    #PBS -l mem=30GB
    #PBS -l walltime=60:00:00
    #PBS -A ccg-ngs
    #PBS -m abe
    #PBS -M .......
    #PBS -o /scratch/ccg-ngs/tmp/v_stdout/${PBS_JOBNAME}.o${PBS_JOBID}
    #PBS -e /scratch/ccg-ngs/tmp/v_stderr/${PBS_JOBNAME}.e${PBS_JOBID}

    #o=$1
    #i=$2
    /projects/ccg-ngs/hthiele0/sw/delly_v0.0.9/delly -o $o $i

    And I submit the job as
    qsub -v o=/scratch/ccg-ngs/tmp/vishal/results/delly/delly2jfidhild.txt,i=/scratch/ccg-ngs/tmp/vishal/results/mrsfast/lag/final.bam /scratch/ccg-ngs/tmp/vishal/results/delly/sample2/delly1.sh



    This doesn't give any output. Even the v_stderr file is empty.
    When I give the path in -o and input instead of $o and $i, the code works.
    What am I doing wrong?

  • #2
    Originally posted by vishal.rossi View Post
    This is the script which I made

    #!/bin/bash -l
    ...
    #o=$1
    #i=$2
    /projects/ccg-ngs/hthiele0/sw/delly_v0.0.9/delly -o $o $i

    And I submit the job as
    qsub -v o=/scratch/ccg-ngs/tmp/vishal/results/delly/delly2jfidhild.txt,i=/scratch/ccg-ngs/tmp/vishal/results/mrsfast/lag/final.bam /scratch/ccg-ngs/tmp/vishal/results/delly/sample2/delly1.sh

    When I give the path in -o and input instead of $o and $i, the code works.
    What am I doing wrong?
    Have you tried not commenting out the "o=$1" and "i=$2" lines? I would assume that those won't be processed by qsub (I use slurm, but assume that qsub is similar enough).

    Comment


    • #3
      Originally posted by dpryan View Post
      Have you tried not commenting out the "o=$1" and "i=$2" lines? I would assume that those won't be processed by qsub (I use slurm, but assume that qsub is similar enough).

      I am sure that #o and #i works and are taken as variables and not comments . But I will try the thing which you suggested and post the result.
      Thank you

      Comment


      • #4
        Originally posted by vishal.rossi View Post
        I am sure that #o and #i works and are taken as variables and not comments . But I will try the thing which you suggested and post the result.
        Thank you
        Are you sure? As far as I know, the syntax of passing info to qsub in scripts follows #$ ..

        What does 'qstat -j yourJobID' say?
        savetherhino.org

        Comment


        • #5
          ok people, the problem is solved

          #!/bin/bash -l
          ##PBS Directives
          #PBS -q default
          #PBS -l nodes=1pn=4
          #PBS -l mem=30GB
          #PBS -l walltime=60:00:00
          #PBS -A ccg-ngs
          #PBS -m abe
          #PBS -M .......
          #PBS -o /scratch/ccg-ngs/tmp/v_stdout/${PBS_JOBNAME}.o${PBS_JOBID}
          #PBS -e /scratch/ccg-ngs/tmp/v_stderr/${PBS_JOBNAME}.e${PBS_JOBID}

          out=$output
          inp=$input
          /projects/ccg-ngs/hthiele0/sw/delly_v0.0.9/delly -o $out $inp

          while submitting the job:
          qsub -v output=/scratch/ccg-ngs/tmp/vishal/results/delly/delly2jfidhild.txt,input=/scratch/ccg-ngs/tmp/vishal/results/mrsfast/lag/final.bam /scratch/ccg-ngs/tmp/vishal/results/delly/sample2/delly1.sh

          Comment

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