#!/bin/bash
#PBS -V
#PBS -N abyss_likrds
#PBS -q batch
#PBS -S /bin/bash
#PBS -m abe
#PBS -e /home/ngutierrez/nas4/abyss/trimgalore_output/with_linkedreads/abyss_likrds.e
#PBS -o /home/ngutierrez/nas4/abyss/trimgalore_output/with_linkedreads/abyss_likrds.o
#PBS -l ncpus=60
#PBS -l walltime=100:00:00
#PBS -l mem=250G
#PBS -M ngutierrez@amnh.org

module load abyss-2.0.2
cd /home/ngutierrez/nas4/abyss/trimgalore_output/with_linkedreads/

abyss-pe k=27 name=Tdiscoideus2 lr='tet' tet='/home/ngutierrez/nas4/linked_reads_output/barcoded.fastq.gz' in='/home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz'



