Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/9da2df51d8a981aca5bcaf978d4d24/aih-tih-sc-973c73-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/d0dc24658992ad5262e17a046d1047/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/d0dc24658992ad5262e17a046d1047/.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/stage-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/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: 428
  Pass (FILTER=PASS): 71 (16.6%)
  Fail (FILTER=FAIL): 357 (83.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 115
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 50
  confidence_below_min(low<high): 43
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6
  total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5

Breakdown by confidence:
  high: 71 pass, 15 fail (total: 86)
  low: 0 pass, 162 fail (total: 162)
  medium: 0 pass, 180 fail (total: 180)
Arriba filter: 428 rows -> 71 PASS; wrote aih-tih-sc-973c73-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-973c73-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-973c73-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt