Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/ff03d5592a72b4db2f2b3b9f9b06b8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/ff03d5592a72b4db2f2b3b9f9b06b8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/ae6ab332b5d60eb252c0a650d143b3/aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-e543dae6-5fea-4720-bfb6-150bf1ff20d4/33/a04540cea7c8abc13163bc03b147d5/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 9 fusion rows (breakpoint_ID in qualified set)

================================================================================
ARRIBA FILTERING SUMMARY
================================================================================

Total fusions: 359
  Pass (FILTER=PASS): 51 (14.2%)
  Fail (FILTER=FAIL): 308 (85.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 71
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 61
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(low<high): 17
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 51 pass, 7 fail (total: 58)
  low: 0 pass, 148 fail (total: 148)
  medium: 0 pass, 153 fail (total: 153)
Arriba filter: 359 rows -> 51 PASS; wrote aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt