Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/99d0672779bf9e1cdc460a3e6558cc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/99d0672779bf9e1cdc460a3e6558cc/.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/48/c50a595d19a527e842740458311437/aih-tih-sc-3270ab-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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 244
  Pass (FILTER=PASS): 33 (13.5%)
  Fail (FILTER=FAIL): 211 (86.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 64
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 20
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 33 pass, 2 fail (total: 35)
  low: 0 pass, 104 fail (total: 104)
  medium: 0 pass, 105 fail (total: 105)
Arriba filter: 244 rows -> 33 PASS; wrote aih-tih-sc-3270ab-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-3270ab-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt