gfa2fa_omnic_hifiasm.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 gfatools_conversion

# Source .bashrc if needed, ensuring no errors if brew isn't found
if [ -f ~/.bashrc ]; then
    source ~/.bashrc || true
fi

# Define variables
INPUT_DIR="/mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/hifiasm_omnic"
OUTPUT_DIR="/mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/gfatools_omnic"

# List of specific GFA files to convert
GFA_FILES=(
    "Sunflower_1_Hetero_Red_withOmniC.asm.hic.hap1.p_ctg.gfa"
    "Sunflower_1_Hetero_Red_withOmniC.asm.hic.hap2.p_ctg.gfa"
    "Sunflower_1_Hetero_Red_withOmniC.asm.hic.p_ctg.gfa"
)

# Loop through each specified GFA file
for FILE in "${GFA_FILES[@]}"; do
    INPUT_GFA="${INPUT_DIR}/${FILE}"
    BASENAME=$(basename ${INPUT_GFA} .gfa)
    OUTPUT_FASTA="${OUTPUT_DIR}/${BASENAME}.fasta"

    # Convert GFA to FASTA
    /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/gfatools_omnic/gfatools/gfatools gfa2fa $INPUT_GFA > $OUTPUT_FASTA

    # Check if gfatools ran successfully for this file
    if [ $? -ne 0 ]; then
        echo "gfatools encountered an error processing ${INPUT_GFA}."
        exit 1
    fi

    echo "gfatools conversion for ${INPUT_GFA} completed successfully."
done