Submit job

1) Create a job-script myJobScript.sh

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, ... )

(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