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demo.sh
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#!/usr/bin/env bash
# Activate Conda environment
source ~/anaconda3/etc/profile.d/conda.sh
conda activate metahit_env
# Define input parameters
SG_R1="./test_data/sim_sg_R1.fastq"
SG_R2="./test_data/sim_sg_R2.fastq"
HIC_R1="./test_data/sim_hic_r1.fq"
HIC_R2="./test_data/sim_hic_r2.fq"
# SG_R1="./test_data/sg1_top20.fastq"
# SG_R2="./test_data/sg2_top20.fastq"
# HIC_R1="./test_data/hic1_top20.fastq"
# HIC_R2="./test_data/hic2_top20.fastq"
OUTPUT_DIR="output"
REFINEMENT_METHOD="metacc"
# Step 1: Read QC
echo "[INFO] Running Read QC for SG sample..."
./metahit.py readqc -1 "$SG_R1" -2 "$SG_R2" -o "${OUTPUT_DIR}/readqc/sg" -t 4 --xmx 4g
echo "[INFO] Running Read QC for Hi-C sample..."
./metahit.py readqc -1 "$HIC_R1" -2 "$HIC_R2" -o "${OUTPUT_DIR}/readqc/hic" -t 4 --xmx 4g
# Step 2: Assembly\
echo "[INFO] Running Assembly with MEGAHIT..."
./metahit.py assembly -1 "${OUTPUT_DIR}/readqc/sg/final_reads_1.fastq.gz" -2 "${OUTPUT_DIR}/readqc/sg/final_reads_2.fastq.gz" \
-o "${OUTPUT_DIR}/assembly" -m 24 -t 4 --megahit --k-min 21 --k-max 141 --k-step 12 -l 1000
# echo "[INFO] Running Assembly with metaSPAdes..."
# ./metahit.py assembly -1 "${OUTPUT_DIR}/readqc/sg/final_reads_1.fastq.gz" \
# -2 "${OUTPUT_DIR}/readqc/sg/final_reads_2.fastq.gz" \
# -o "${OUTPUT_DIR}/assembly" --metaflye --method nano-hq
# Step 3: Alignment
echo "[INFO] Running Alignment..."
./metahit.py alignment -r "${OUTPUT_DIR}/assembly/final_assembly.fasta" \
-1 "${OUTPUT_DIR}/readqc/hic/final_reads_1.fastq.gz" -2 "${OUTPUT_DIR}/readqc/hic/final_reads_2.fastq.gz" \
-o "${OUTPUT_DIR}/alignment" --threads 4 --samtools-filter '-F 0x904'
# Step 4: Coverage Estimation
echo "[INFO] Running Coverage Estimation..."
./metahit.py coverage_estimation -1 "$SG_R1" -2 "$SG_R2" \
-r "${OUTPUT_DIR}/assembly/final_assembly.fasta" -o "${OUTPUT_DIR}/estimation"
# Step 5: Raw Contact Generation
echo "[INFO] Generating Raw Contacts..."
./metahit.py raw_contact \
--bam "${OUTPUT_DIR}/alignment/sorted_map.bam" \
--fasta "${OUTPUT_DIR}/assembly/final_assembly.fasta" \
--out "${OUTPUT_DIR}/normalization/raw" \
--enzyme "HindIII"
# Step 6: Normalization with optional refinement
echo "[INFO] Running Normalization"
for method in raw normcc hiczin bin3c metator fastnorm; do
output_dir="${OUTPUT_DIR}/normalization/${method}"
# Ensure output directory exists
mkdir -p "$output_dir"
case $method in
raw)
./metahit.py normalization raw --contig_file "${OUTPUT_DIR}/normalization/raw/contig_info.csv" \
--contact_matrix_file "${OUTPUT_DIR}/normalization/raw/raw_contact_matrix_metacc.npz" \
--output "${OUTPUT_DIR}/normalization/raw" --min_len 500 --min_signal 1 --thres 1
;;
normcc)
echo "[INFO] Running NormCC Normalization"
./metahit.py normalization $method --contig_file "${OUTPUT_DIR}/normalization/raw/contig_info.csv" \
--contact_matrix_file "${OUTPUT_DIR}/normalization/raw/raw_contact_matrix_metacc.npz" \
--output "${OUTPUT_DIR}/normalization/${method}" --thres 1
;;
hiczin)
echo "[INFO] Running HiCzin Normalization"
./metahit.py normalization $method --contig_file "${OUTPUT_DIR}/normalization/raw/contig_info.csv" \
--contact_matrix_file "${OUTPUT_DIR}/normalization/raw/raw_contact_matrix_metacc.npz" \
--output "${OUTPUT_DIR}/normalization/${method}" --thres 1 --epsilon 1
;;
metator)
echo "[INFO] Running Metator Normalization"
./metahit.py normalization $method --contig_file "${OUTPUT_DIR}/normalization/raw/contig_info.csv" \
--contact_matrix_file "${OUTPUT_DIR}/normalization/raw/raw_contact_matrix_metacc.npz" \
--output "${OUTPUT_DIR}/normalization/${method}" --thres 1 --epsilon 1
;;
bin3c)
echo "[INFO] Running Bin3C Normalization"
./metahit.py normalization bin3c --contig_file "${OUTPUT_DIR}/normalization/raw/contig_info.csv" \
--contact_matrix_file "${OUTPUT_DIR}/normalization/raw/raw_contact_matrix_metacc.npz" \
--output "${OUTPUT_DIR}/normalization/bin3c" --max_iter 1000 --tol 1e-6 --thres 1
;;
fastnorm)
echo "[INFO] Running FastNorm Normalization"
./metahit.py normalization fastnorm --contig_file "${OUTPUT_DIR}/normalization/raw/contig_info.csv" \
--contact_matrix_file "${OUTPUT_DIR}/normalization/raw/raw_contact_matrix_metacc.npz" \
--output "${OUTPUT_DIR}/normalization/fastnorm" --epsilon 1 --thres 1
;;
esac
if [ $? -ne 0 ]; then
echo "[ERROR] Normalization failed for method $method."
exit 1
fi
done
# Step 7: Bin Refinement
echo "[INFO] Running Bin Refinement Process..."
./metahit.py bin_refinement --fasta "${OUTPUT_DIR}/assembly/final_assembly.fasta" \
--bam "${OUTPUT_DIR}/alignment/sorted_map.bam" \
--output "${OUTPUT_DIR}/bins/" \
-t 10 \
--enzyme DpnII \
--metacc-min-len 1000 \
--metacc-min-signal 2 \
--bin3c-min-len 1000 \
--bin3c-min-signal 1 \
--thres 0.01 \
--cover
# Scaffolding
echo "[INFO] Running Scaffolding..."
./metahit.py scaffolding \
--fasta "${OUTPUT_DIR}/assembly/final_assembly.fasta" \
--bam "${OUTPUT_DIR}/alignment/sorted_map.bam" \
--enzyme "HindIII" \
--hic1 "$HIC_R1" \
--hic2 "$HIC_R2" \
-o "${OUTPUT_DIR}/scaffolding" \
-t 4 -m 24 -r 10000
# Reassembly
echo "[INFO] Running Reassembly..."
./metahit.py reassembly \
--bin "${OUTPUT_DIR}/bins" \
--hic1 "${OUTPUT_DIR}/readqc/hic/final_reads_1.fastq.gz" \
--hic2 "${OUTPUT_DIR}/readqc/hic/final_reads_2.fastq.gz" \
--sg1 "${OUTPUT_DIR}/readqc/sg/final_reads_1.fastq.gz" \
--sg2 "${OUTPUT_DIR}/readqc/sg/final_reads_2.fastq.gz" \
--bam "${OUTPUT_DIR}/alignment/sorted_map.bam" \
--outdir "${OUTPUT_DIR}/reassembly" \
-p "$(pwd)" \
-t 4 -m 24
# Viral CC
# TODO: change viral_contigs.txt file
echo "[INFO] Running ViralCC pipeline..."
./metahit.py viralcc pipeline\
"${OUTPUT_DIR}/assembly/final_assembly.fasta" \
"${OUTPUT_DIR}/alignment/sorted_map.bam" \
"./test_data/viral_contigs.txt" \
"${OUTPUT_DIR}/viralcc"
echo "[INFO] Running GTDB-Tk annotation..."
./metahit.py annotation \
--genome_dir "${OUTPUT_DIR}/assembly/final_assembly.fasta" \
--out_dir "${OUTPUT_DIR}/annotation" \
--extension fa \
--cpus 60
# TODO CHANGE THE FILES
# ./metahit.py bin_plot \
# --contact-map "path/to/contact_map.pkl" \
# --BIN "path/to/clustering_result.bin" \
# --OUTDIR "${OUTPUT_DIR}/bin_plot"
# TODO CHANGE THE FILES, repleace it by the real paths
./metahit.py virus_host_interaction \
--BIN "path/to/binning_result.txt" \
--viral-contig "path/to/viral_contig_list.txt" \
--contact "path/to/contact_matrix" \
--OUTDIR "output/virus_host_interaction" \
-t 8 -m 32
./metahit.py genomad --genome_file ${OUTPUT_DIR}/readqc/hic/final_reads_1.fastq.gz -o output/genomad -s 16