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tasks/genome-completeness/run_script.sh

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+#!/bin/bash
+set -e
+
+# =============================================================================
+# Task 29: Genome Completeness and Contamination Assessment
+#
+# DAG (depth 5):
+# L0: assembled genome
+# L1: ├── BUSCO (single-copy orthologs)
+#     ├── QUAST (assembly metrics)
+#     └── Prokka (gene prediction for stats)
+# L2: ├── seqkit stats (basic stats)
+#     └── parse BUSCO/QUAST/Prokka outputs
+# L3: checkv (if viral) OR manual assessment
+# L4: MERGE (comprehensive quality report)
+# =============================================================================
+
+THREADS=$(( $(nproc) > 8 ? 8 : $(nproc) ))
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+DATA="${SCRIPT_DIR}/data"
+REF="${SCRIPT_DIR}/reference"
+OUT="${SCRIPT_DIR}/outputs"
+RES="${SCRIPT_DIR}/results"
+
+GENOME="${DATA}/genome.fna"
+REFERENCE="${REF}/reference.fna"
+
+log_step() {
+    echo "=================================================================="
+    echo "STEP: $1"
+    echo "$(date)"
+    echo "=================================================================="
+}
+
+mkdir -p "${OUT}"/{busco_out,quast,prokka,stats} "${RES}"
+
+# L1-A: BUSCO
+log_step "L1-A: BUSCO"
+if [ ! -d "${OUT}/busco_out/busco" ]; then
+    busco -i "${GENOME}" -o busco --out_path "${OUT}/busco_out" \
+          -l bacteria_odb10 -m genome -c ${THREADS} --force
+else echo "Skipping (exists)"; fi
+
+# L1-B: QUAST with reference
+log_step "L1-B: QUAST"
+if [ ! -f "${OUT}/quast/report.tsv" ]; then
+    quast "${GENOME}" -r "${REFERENCE}" -o "${OUT}/quast" -t ${THREADS}
+else echo "Skipping (exists)"; fi
+
+# L1-C: Prokka
+log_step "L1-C: Prokka"
+if [ ! -f "${OUT}/prokka/genome.gff" ]; then
+    prokka "${GENOME}" --outdir "${OUT}/prokka" --prefix genome \
+           --cpus ${THREADS} --kingdom Bacteria --force
+else echo "Skipping (exists)"; fi
+
+# L2: seqkit + parse
+log_step "L2: Parse results"
+
+seqkit stats "${GENOME}" -T > "${OUT}/stats/seqkit.tsv"
+
+# BUSCO
+BUSCO_SUM=$(grep "C:" "${OUT}/busco_out/busco/short_summary.specific.bacteria_odb10.busco.txt" 2>/dev/null \
+    | head -1 | sed 's/^[[:space:]]*//' || echo "N/A")
+BUSCO_COMPLETE=$(echo "$BUSCO_SUM" | grep -oP 'C:[\d.]+' | tr -d 'C:')
+BUSCO_FRAGMENTED=$(echo "$BUSCO_SUM" | grep -oP 'F:[\d.]+' | tr -d 'F:')
+BUSCO_MISSING=$(echo "$BUSCO_SUM" | grep -oP 'M:[\d.]+' | tr -d 'M:')
+
+# QUAST
+TOTAL_LEN=$(grep "^Total length" "${OUT}/quast/report.tsv" | head -1 | cut -f2)
+NUM_CONTIGS=$(grep "^# contigs " "${OUT}/quast/report.tsv" | head -1 | cut -f2)
+N50=$(grep "^N50" "${OUT}/quast/report.tsv" | cut -f2)
+GC=$(grep "^GC" "${OUT}/quast/report.tsv" | cut -f2)
+LARGEST=$(grep "^Largest contig" "${OUT}/quast/report.tsv" | cut -f2)
+GF=$(grep "^Genome fraction" "${OUT}/quast/report.tsv" | cut -f2)
+MISASSEMBLIES=$(grep "^# misassemblies" "${OUT}/quast/report.tsv" | cut -f2)
+DUPLICATION=$(grep "^Duplication ratio" "${OUT}/quast/report.tsv" | cut -f2)
+
+# Prokka
+CDS=$(grep "^CDS" "${OUT}/prokka/genome.txt" | awk '{print $2}')
+TRNA=$(grep "^tRNA" "${OUT}/prokka/genome.txt" | awk '{print $2}')
+RRNA=$(grep "^rRNA" "${OUT}/prokka/genome.txt" | awk '{print $2}')
+CODING_DENSITY=$(python3 -c "
+cds_len = 0
+for line in open('${OUT}/prokka/genome.gff'):
+    if '\tCDS\t' in line:
+        parts = line.split('\t')
+        cds_len += int(parts[4]) - int(parts[3]) + 1
+print(f'{cds_len/${TOTAL_LEN}*100:.1f}')
+" 2>/dev/null || echo "N/A")
+
+# L4: MERGE
+log_step "L4-MERGE"
+
+cat > "${RES}/completeness_report.csv" << CSVEOF
+metric,value
+total_length,${TOTAL_LEN}
+num_contigs,${NUM_CONTIGS}
+n50,${N50}
+gc_content,${GC}
+largest_contig,${LARGEST}
+genome_fraction,${GF}
+misassemblies,${MISASSEMBLIES}
+duplication_ratio,${DUPLICATION}
+busco_complete_pct,${BUSCO_COMPLETE}
+busco_fragmented_pct,${BUSCO_FRAGMENTED}
+busco_missing_pct,${BUSCO_MISSING}
+cds_count,${CDS}
+trna_count,${TRNA}
+rrna_count,${RRNA}
+coding_density_pct,${CODING_DENSITY}
+CSVEOF
+
+echo ""
+echo "=== Pipeline complete ==="
+cat "${RES}/completeness_report.csv"