Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/ca9e1d2bc4ccd8d78ec8c5a1c01b71/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/ca9e1d2bc4ccd8d78ec8c5a1c01b71/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/c1003da2045fe33fbf34da89fc27a6/aih-tih-sc-f834a3-R1_A23YTGFLT4_1.arriba.fusions.tsv
  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-e543dae6-5fea-4720-bfb6-150bf1ff20d4/33/a04540cea7c8abc13163bc03b147d5/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 242
  Pass (FILTER=PASS): 23 (9.5%)
  Fail (FILTER=FAIL): 219 (90.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 42
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 33
  confidence_below_min(low<high): 28
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(medium<high): 24
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 23 pass, 2 fail (total: 25)
  low: 0 pass, 130 fail (total: 130)
  medium: 0 pass, 87 fail (total: 87)
Arriba filter: 242 rows -> 23 PASS; wrote aih-tih-sc-f834a3-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-f834a3-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-f834a3-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt