omnic_gfastats_h2.pbs

#!/bin/bash
#PBS -q condo05
#PBS -l select=1:ncpus=32:mem=250GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N gfastats_conversion

# Define variables
INPUT_GFA="/mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/hifiasm_omnic/Sunflower_1_Hetero_Red_withOmniC.asm.hic.hap2.p_ctg.gfa"
OUTPUT_DIR="/mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/gfastats_output"
OUTPUT_FASTA="${OUTPUT_DIR}/Sunflower_1_Hetero_Red_withOmniC_hap2_pcontig.fasta"
GFASTATS_BIN="/mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/gfastats/build/bin/gfastats"

# Check if gfastats binary exists
if [ ! -x $GFASTATS_BIN ]; then
    echo "Error: gfastats binary not found or not executable at $GFASTATS_BIN"
    exit 1
fi

# Run gfastats to convert GFA to FASTA and generate statistics
$GFASTATS_BIN $INPUT_GFA -o $OUTPUT_FASTA

# Check if gfastats ran successfully
if [ $? -ne 0 ]; then
    echo "gfastats encountered an error."
    exit 1
fi

echo "gfastats conversion completed successfully."