Hi,
Does anybody here has an experience of submitting jobs with slurm scheduler.
My code is like this (an example) :
#########################################
#!/bin/bash -l
#SBatch -p default
#SBatch -N 1
#SBatch -n 1
#SBatch --mem-per-cpu=5gb
#SBatch --cpus-per-task=1
#SBatch -t 00:02:00
inp1=$inp
sid=$id
echo inp1:$inp1
echo sid:$sid
python /sw/conifer_v0.2.2/conifer.py rpkm --probes /sw/conifer_v0.2.2/sampledata/probes.txt --input $inp1 --output /conifer/control/rpkm/$sid.rpkm.txt
############################################
It's saved as script.sh.
I call the script from the terminal using :
sbatch script.sh inp AID2831_SID6849_21909_normal.Improved.bam id AID2831_SID6849_21909_normal
The code runs and then fails as it says that it couldn't find the input file.
even echo inp1:$inp1 shows that it's empty.
But when I hard code the inp and id in the code, I am able to run the script.
Does anyone knows where I am going wrong.
Thanks in advance.
Regards
Vishal
Does anybody here has an experience of submitting jobs with slurm scheduler.
My code is like this (an example) :
#########################################
#!/bin/bash -l
#SBatch -p default
#SBatch -N 1
#SBatch -n 1
#SBatch --mem-per-cpu=5gb
#SBatch --cpus-per-task=1
#SBatch -t 00:02:00
inp1=$inp
sid=$id
echo inp1:$inp1
echo sid:$sid
python /sw/conifer_v0.2.2/conifer.py rpkm --probes /sw/conifer_v0.2.2/sampledata/probes.txt --input $inp1 --output /conifer/control/rpkm/$sid.rpkm.txt
############################################
It's saved as script.sh.
I call the script from the terminal using :
sbatch script.sh inp AID2831_SID6849_21909_normal.Improved.bam id AID2831_SID6849_21909_normal
The code runs and then fails as it says that it couldn't find the input file.
even echo inp1:$inp1 shows that it's empty.
But when I hard code the inp and id in the code, I am able to run the script.
Does anyone knows where I am going wrong.
Thanks in advance.
Regards
Vishal
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