Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/0236d4ae39e4826236272cb4c9d2c1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/dd0fbc2867aacde12be38890c56781/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/dd0fbc2867aacde12be38890c56781/.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-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 132
  Pass (FILTER=PASS): 22 (16.7%)
  Fail (FILTER=FAIL): 110 (83.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(low<high): 7
  confidence_below_min(medium<high): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);aih_curated_blacklist: 3
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 22 pass, 4 fail (total: 26)
  low: 0 pass, 36 fail (total: 36)
  medium: 0 pass, 70 fail (total: 70)
Arriba filter: 132 rows -> 22 PASS; wrote aih-tih-sc-19e09e-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-19e09e-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt