Upload tasks/phage-characterization/run_script.sh with huggingface_hub

tasks/phage-characterization/run_script.sh

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+#!/bin/bash
+set -e
+
+# =============================================================================
+# Task 21: Phage Genome Characterization
+#
+# DAG (depth 5, fan-out from assembly):
+#
+# L0: reads
+# L1: fastp (trim)
+# L2: shovill (assemble)
+#     ├────────────────────────────────────────┐
+# L3: pharokka (phage annotation)       checkv (quality)
+#     │                                        │
+# L4: functional summary                 completeness report
+#     │                                        │
+#     ├── abricate VFDB (virulence)            │
+#     └────────────────────────────────────────┘
+# L5: MERGE
+# =============================================================================
+
+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"
+
+PHAROKKA_DB="/pscratch/sd/l/lingzhi/pharokka_db"
+CHECKV_DB="/pscratch/sd/l/lingzhi/checkv_db/checkv-db-v1.5"
+
+log_step() {
+    echo "=================================================================="
+    echo "STEP: $1"
+    echo "$(date)"
+    echo "=================================================================="
+}
+
+mkdir -p "${OUT}"/{trimmed,assembly,pharokka,checkv,vfdb} "${RES}"
+
+# ===========================================================================
+# L1: Trimming
+# ===========================================================================
+log_step "L1: fastp"
+if [ ! -f "${OUT}/trimmed/R1.fastq.gz" ]; then
+    fastp --in1 "${DATA}/reads_R1.fastq.gz" --in2 "${DATA}/reads_R2.fastq.gz" \
+          --out1 "${OUT}/trimmed/R1.fastq.gz" --out2 "${OUT}/trimmed/R2.fastq.gz" \
+          --detect_adapter_for_pe --thread ${THREADS} \
+          --json "${OUT}/trimmed/fastp.json"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L2: Assembly
+# ===========================================================================
+log_step "L2: MEGAHIT assembly"
+if [ ! -f "${OUT}/assembly/final.contigs.fa" ]; then
+    megahit -1 "${OUT}/trimmed/R1.fastq.gz" -2 "${OUT}/trimmed/R2.fastq.gz" \
+            -o "${OUT}/assembly" -t ${THREADS} --min-contig-len 500
+else echo "Skipping (exists)"; fi
+CONTIGS="${OUT}/assembly/final.contigs.fa"
+
+# ===========================================================================
+# L3-A: Pharokka phage-specific annotation
+# ===========================================================================
+log_step "L3-A: pharokka annotation"
+if [ ! -f "${OUT}/pharokka/pharokka_final.gff" ]; then
+    pharokka.py -i "${CONTIGS}" -o "${OUT}/pharokka" \
+                -d "${PHAROKKA_DB}" -t ${THREADS} --force 2>&1 || {
+        echo "WARNING: pharokka failed, falling back to prokka --kingdom Viruses"
+        prokka "${CONTIGS}" --outdir "${OUT}/pharokka" --prefix pharokka_final \
+               --cpus ${THREADS} --kingdom Viruses --force 2>&1 || true
+    }
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L3-B: CheckV quality assessment
+# ===========================================================================
+log_step "L3-B: checkv quality"
+if [ ! -f "${OUT}/checkv/quality_summary.tsv" ]; then
+    if [ -d "${CHECKV_DB}" ]; then
+        checkv end_to_end "${CONTIGS}" "${OUT}/checkv" -d "${CHECKV_DB}" -t ${THREADS} 2>&1 || true
+    else
+        echo "WARNING: CheckV database not found"
+        mkdir -p "${OUT}/checkv"
+        touch "${OUT}/checkv/quality_summary.tsv"
+    fi
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L3-C: Virulence factor detection
+# ===========================================================================
+log_step "L3-C: abricate VFDB"
+if [ ! -f "${OUT}/vfdb/vfdb_results.tsv" ]; then
+    abricate "${CONTIGS}" --db vfdb --minid 80 --mincov 60 > "${OUT}/vfdb/vfdb_results.tsv" 2>/dev/null || true
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L4: Parse results
+# ===========================================================================
+log_step "L4: Parse annotation results"
+
+# Pharokka stats
+PHAROKKA_GFF="${OUT}/pharokka/pharokka.gff"
+if [ -f "${PHAROKKA_GFF}" ]; then
+    CDS=$(grep -c "CDS" "${PHAROKKA_GFF}" 2>/dev/null || echo "0")
+    TRNA=$(grep -c "tRNA" "${OUT}/pharokka/pharokka_aragorn.gff" 2>/dev/null || true)
+    TRNA=${TRNA:-0}
+    # Count functional categories from pharokka GFF product annotations
+    LYSIS=$(grep -ic "lysis\|holin\|endolysin\|spanin\|lysozyme" "${PHAROKKA_GFF}" 2>/dev/null || echo "0")
+    LYSOGENY=$(grep -ic "integrase\|repressor\|lysogeny\|excisionase" "${PHAROKKA_GFF}" 2>/dev/null || echo "0")
+    REPLICATION=$(grep -ic "helicase\|primase\|polymerase\|replication\|SSB" "${PHAROKKA_GFF}" 2>/dev/null || echo "0")
+    STRUCTURAL=$(grep -ic "capsid\|tail\|baseplate\|head\|portal\|sheath\|fiber" "${PHAROKKA_GFF}" 2>/dev/null || echo "0")
+    # Get top MASH hit for taxonomy
+    TAXONOMY=$(tail -1 "${OUT}/pharokka/pharokka_top_hits_mash_inphared.tsv" 2>/dev/null | cut -f6 || echo "Unknown")
+else
+    CDS=0; TRNA=0; LYSIS=0; LYSOGENY=0; REPLICATION=0; STRUCTURAL=0; TAXONOMY="Unknown"
+fi
+
+# CheckV stats
+if [ -s "${OUT}/checkv/quality_summary.tsv" ]; then
+    QUALITY=$(tail -1 "${OUT}/checkv/quality_summary.tsv" | cut -f8 || echo "N/A")
+    COMPLETENESS=$(tail -1 "${OUT}/checkv/quality_summary.tsv" | cut -f10 || echo "N/A")
+    CONTAMINATION=$(tail -1 "${OUT}/checkv/quality_summary.tsv" | cut -f12 || echo "N/A")
+else
+    QUALITY="N/A"; COMPLETENESS="N/A"; CONTAMINATION="N/A"
+fi
+
+# Assembly stats
+NUM_CONTIGS=$(grep -c ">" "${CONTIGS}" || echo "0")
+TOTAL_LEN=$(awk '/^>/{if(l)print l; l=0; next}{l+=length}END{print l}' "${CONTIGS}" || echo "0")
+GC=$(awk '/^>/{next}{s+=length; gc+=gsub(/[GCgc]/,"&")}END{printf "%.2f",gc/s*100}' "${CONTIGS}" || echo "0")
+
+# Virulence
+VF_COUNT=$(tail -n +2 "${OUT}/vfdb/vfdb_results.tsv" 2>/dev/null | wc -l | tr -d ' ' || echo "0")
+
+# ===========================================================================
+# L5: MERGE
+# ===========================================================================
+log_step "L5-MERGE"
+
+cat > "${RES}/phage_report.csv" << CSVEOF
+metric,value
+genome_length,${TOTAL_LEN}
+num_contigs,${NUM_CONTIGS}
+gc_content,${GC}
+closest_hit,${TAXONOMY}
+cds_count,${CDS}
+trna_count,${TRNA}
+lysis_genes,${LYSIS}
+lysogeny_genes,${LYSOGENY}
+replication_genes,${REPLICATION}
+structural_genes,${STRUCTURAL}
+checkv_quality,${QUALITY}
+checkv_completeness,${COMPLETENESS}
+virulence_factors,${VF_COUNT}
+CSVEOF
+
+echo ""
+echo "=== Pipeline complete ==="
+cat "${RES}/phage_report.csv"
+echo ""
+ls -lh "${RES}/"