hifiasm_omnic.pbs

#!/bin/bash
#PBS -q beta
#PBS -l select=1:ncpus=36:mem=1509GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N HifiasmMutagenesisSunflowerAssembly

cd /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha

/mmfs1/projects/brent.hulke/Software/hifiasm/hifiasm -o Sunflower_1_Hetero_Red_withOmniC.asm \
                                                     -t 36 \
                                                     --h1 LAID_OmniC_NA_NA_TTCCAAGG_Sunflower_Hetero_Red-Sunflower_OmniC_I1381_L1_R1.fastq.gz \ 
                                                     --h2 LAID_OmniC_NA_NA_TTCCAAGG_Sunflower_Hetero_Red-Sunflower_OmniC_I1381_L1_R2.fastq.gz \ 
                                                     /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/MutagenesisPacBioLongReadsMerged.fastq.gz \
                                                     > ./hifiasm_omnic/hifiasmMutagenesis_omnic_log.txt 2>&1