Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/54fb7895043f34ae2881294d1a67a1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/885a7643694b03a5eaf7f4e50ae9c0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/885a7643694b03a5eaf7f4e50ae9c0/.command.sh
  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 16 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 214
  Pass (FILTER=PASS): 27 (12.6%)
  Fail (FILTER=FAIL): 187 (87.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 16
  All 16 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 69
  confidence_below_min(low<high): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  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(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  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): 3
  confidence_below_min(low<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 27 pass, 2 fail (total: 29)
  low: 0 pass, 85 fail (total: 85)
  medium: 0 pass, 100 fail (total: 100)
Arriba filter: 214 rows -> 27 PASS; wrote aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-13d441-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt