New to BAsh. Encountered an error

[vishal.rossi]

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?

[dpryan]

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).

[vishal.rossi]

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

[rhinoceros]

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?

[vishal.rossi]

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