Running a command on SLURM that takes command-line arguments - bash

Question

I'm completely new to using HPCs and SLURM, so I'd really appreciate some guidance here.
I need to iteratively run a command that looks like this
kallisto quant -i '/home/myName/genomes/hSapien.idx' \
-o "output-SRR3225412" \
"SRR3225412_1.fastq.gz" \
"SRR3225412_2.fastq.gz"
where the SRR3225412 part will be different in each interation
The problem is, as I found out, I can't just append this to the end of an sbatch command
sbatch --nodes=1 \
--ntasks-per-node=1 \
--cpus-per-task=1 \
kallisto quant -i '/home/myName/genomes/hSapien.idx' \
-o "output-SRR3225412" \
"SRR3225412_1.fastq.gz" \
"SRR3225412_2.fastq.gz"
This command doesn't work. I get the error
sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
I wanted to ask, how do I run the sbatch command, specifying its run parameters, and also adding the command-line arguments for the kallisto program I'm trying to use? In the end I'd like to have something like
#!/bin/bash
for sample in ...
do
sbatch --nodes=1 \
--ntasks-per-node=1 \
--cpus-per-task=1 \
kallistoCommandOnSample --arg1 a1 \
--arg2 a2 arg3 a3
done

Answer 1

The error sbatch: error: This does not look like a batch script. is because sbatch expect a submission script. It is a batch script, typically a Bash script, in which comments starting with #SBATCH are interpreted by Slurm as options.
So the typical way of submitting a job is to create a file, let's name it submit.sh:
#! /bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
kallisto quant -i '/home/myName/genomes/hSapien.idx' \
-o "output-SRR3225412" \
"SRR3225412_1.fastq.gz" \
"SRR3225412_2.fastq.gz"
and then submit it with
sbatch submit.sh
If you have multiple similar jobs to submit, it is beneficial for several reasons to use a job array. The loop you want to create can be replaced with a single submission script looking like
#! /bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --array=1-10 # Replace here with the number of iterations in the loop
SAMPLES=(...) # here put what you would loop over
CURRSAMPLE=${SAMPLE[$SLURM_ARRAY_TASK_ID]}
kallisto quant -i '/home/myName/genomes/hSapien.idx' \
-o "output-${CURRSAMPLE}" \
"${CURRSAMPLE}_1.fastq.gz" \
"${CURRSAMPLE}_2.fastq.gz"
As pointed out by #Carles Fenoy, if you do not want to use a submission script, you can use the --wrap parameter of sbatch:
sbatch --nodes=1 \
--ntasks-per-node=1 \
--cpus-per-task=1 \
--wrap "kallisto quant -i '/home/myName/genomes/hSapien.idx' \
-o 'output-SRR3225412' \
'SRR3225412_1.fastq.gz' \
'SRR3225412_2.fastq.gz'"