Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/bd1a54535b00c01cd801f536390d7a/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/2b1b76fb0b0da8ca6de743dc848c87/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/2b1b76fb0b0da8ca6de743dc848c87/.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 217
  Pass (FILTER=PASS): 37 (17.1%)
  Fail (FILTER=FAIL): 180 (82.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 60
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 37 pass, 3 fail (total: 40)
  low: 0 pass, 90 fail (total: 90)
  medium: 0 pass, 87 fail (total: 87)
Arriba filter: 217 rows -> 37 PASS; wrote aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt