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 $i, the code works.
What am I doing wrong?
#!/bin/bash -l
##PBS Directives
#PBS -q default
#PBS -l nodes=1pn=4
#PBS -l mem=30GB
#PBS -l walltime=60:00:00
#PBS -A ccg-ngs
#PBS -m abe
#PBS -M .......
#PBS -o /scratch/ccg-ngs/tmp/v_stdout/${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?
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