yakHomo.pbs

#!/bin/bash
#PBS -q condo05
#PBS -l select=1:ncpus=64:mem=250GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke

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

# Run yak on the two homozygous red fastq files (PCRfree, Illumina short reads)
# Output: HomoRed.yak, HomoRedYak_log.txt
/mmfs1/home/brian.smart/software/yak/yak count -k31 -b37 -t32 -o Sunflower_2_Homo_Red.yak Sunflower_2_Homo_Red_R1_fastp.fastq.gz Sunflower_2_Homo_Red_R2_fastp.fastq.gz > Sunflower_2_Homo_Red_yakLog.txt 2>&1 &

# Run yak on the two homozygous green fastq files (PCRfree, Illumina short reads)
# Output: HomoGreen.yak, HomoGreenYak_log.txt
/mmfs1/home/brian.smart/software/yak/yak count -k31 -b37 -t32 -o Sunflower_3_Homo_Green.yak Sunflower_3_Homo_Green_R1_fastp.fastq.gz Sunflower_3_Homo_Green_R2_fastp.fastq.gz > Sunflower_3_Homo_Green_yakLog.txt 2>&1

wait