Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/0e93e00890fbcce73129d21f2822a4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/0e93e00890fbcce73129d21f2822a4/.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/ca/6e05c2d4feff8496f9a136697d5bc1/aih-tih-sc-6ff823-R1_A23WJ53LT4_1.arriba.fusions.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: 221
  Pass (FILTER=PASS): 22 (10.0%)
  Fail (FILTER=FAIL): 199 (90.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 37
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  total_reads_below_min(4.0<8.0): 5
  total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3

Breakdown by confidence:
  high: 22 pass, 10 fail (total: 32)
  low: 0 pass, 78 fail (total: 78)
  medium: 0 pass, 111 fail (total: 111)
Arriba filter: 221 rows -> 22 PASS; wrote aih-tih-sc-6ff823-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-6ff823-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-6ff823-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt