assembly-pipeline.sb

#!/bin/bash -login
#SBATCH --time=160:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12
#SBATCH --mem=400G
#SBATCH --job-name assembly
#SBATCH --mail-type=ALL
#SBATCH --mail-user=howead@msu.edu
#SBATCH --account shadeash-colej

MY_PATH=/mnt/scratch/howead/tomas-metag-pipeline
ASSEMBLER_PATH=/mnt/home/howead//software/megahit-1.1.3/
THREADS=12
MEM=400e9
TRIMMED_READS_PATH=/mnt/scratch/howead/tomas-metag-pipeline/trimmed-reads
PAR_PATH=~/software/parallel-20180922/src/

cd $MY_PATH
#echo "cat $TRIMMED_READS_PATH/*pe1 >> $TRIMMED_READS_PATH/pe1.fq" > pre-assembly-wrangle.sh
#echo "cat $TRIMMED_READS_PATH/*pe2 >> $TRIMMED_READS_PATH/pe2.fq" >> pre-assembly-wrangle.sh
#echo "cat $TRIMMED_READS_PATH/*se12 >> $TRIMMED_READS_PATH/se12.fq" >> pre-assembly-wrangle.sh
#cat pre-assembly-wrangle.sh | $PAR_PATH/parallel
echo "$ASSEMBLER_PATH/megahit --kmin-1pass -1 $TRIMMED_READS_PATH/pe1.fq -2 $TRIMMED_READS_PATH/pe2.fq -r $TRIMMED_READS_PATH/se12.fq --presets meta-large -o assembly -m $MEM" > megahit.sh
bash megahit.sh