Job-script contains the HPC queue settings (queue name, log-files, email, ...) and the main tool command (e.g. echo, BLAST, bowtie2, ... )
#!/bin/bash
#
# SGE SETTINGS
#$ -q std.q # queue name to which script will be submitted
#$ -N ReadAlign # script name to be visible in the queue
#$ -o /my/new/project/log_output_$JOB_ID.txt # command output file in project path
#$ -e /my/new/project/log_error_$JOB_ID.txt # command error message file
#$ -M my.email.address@gmail.com # to get notifications about script status
#$ -m ea # send email in case of job end or abort(error)
#$ -pe smp 8 # number of required processors
#
# TOOL COMMANDS
# go to working directory
cd /my/new/project/
# print computer name (host-name of selected cluster node)
echo "Hello from `hostname`!"
# run main tool command
singularity exec /my/tools/bowtie2-2.5.1.sif bowtie2 -x ecoli -1 SAMPLE_R1.fastq -2 SAMPLE_R2.fastq --no-unal -p 8 -S SAMPLE.sam
# submit a job-script ( add “myJobScript.sh” as new job to queue “std.q” )
qsub myJobScript.sh
# check status of all my submitted jobs ( Is my job still waiting in queue or already running? )
qstat -f
# show jobs of all users ( all running and waiting jobs)
qstat -u '*' -f | more
r - job-script is running
qw - waiting in the queue
Eqw - Error in script, job is not executed, check possible error (disk quota, file permission, ... )
→ Check resources of the nodes in a HPC SGE cluster
(1) get job-ID
qstat
job-ID priority job-name user state queue
12345 0.750 ReadAlign myName r std.q@node2.cluster
(2) delete job ( remove an already submitted job-script )
qdel 12345