Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/4b93decad86818bd7acee419dc4091/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/ecc5cc62ed6aa74d8fc2df87038e14/aih-tih-sc-64cace-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/4b93decad86818bd7acee419dc4091/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 166
  Pass (FILTER=PASS): 31 (18.7%)
  Fail (FILTER=FAIL): 135 (81.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 57
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(4.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 31 pass, 2 fail (total: 33)
  low: 0 pass, 51 fail (total: 51)
  medium: 0 pass, 82 fail (total: 82)
Arriba filter: 166 rows -> 31 PASS; wrote aih-tih-sc-64cace-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-64cace-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-64cace-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt