C2a1_submit_masurca.sh

#!/bin/sh
#PBS -W group_list=ku_00039 -A ku_00039
#PBS -m n
#PBS -l nodes=1:ppn=40
#PBS -l mem=190gb
#PBS -l walltime=96:00:00


# Go to the directory from where the job was submitted (initial directory is $HOME)
echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR

### Here follows the user commands:
# Define number of processors
NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes

# Load all required modules for the job
module load tools
module load ngs
module load masurca/3.3.0


# This is where the work is done
# Make sure that this script is not bigger than 64kb ~ 150 lines, otherwise put in seperat script and execute from here


# First run masurca on the config file: masurca config.txt, then submit this job.

bash assemble.sh