busco_omnic_embryophyta.pbs

#!/bin/bash
#PBS -q bigmem
#PBS -l select=1:ncpus=64:mem=500GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N funTimesWithBUSCO

#download the lineage dataset first into the directory which is set in the following step 

# Set directory
cd /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiOmniCAssembly/busco_embryophyta 
 
# Load conda environment
source /mmfs1/home/senta.kryzer/miniconda3/bin/activate busco_env
 
#Run busco
busco -i /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiOmniCAssembly/gfatools_omnic/Sunflower_1_Hetero_Red_withOmniC.asm.hic.p_ctg.fasta \
      -m genome \
      -c 64 \
      -l /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiOmniCAssembly/busco_embryophyta/busco_downloads/lineages/embryophyta_odb10 \
      --offline \
      -o omnic_embryophyta_odb10