Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/2db1faa28e728b9e64418608fe17b3/aih-tih-sc-98fc22-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/ae5952b10fabf4e4f2e0b96ed7b8f7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/ae5952b10fabf4e4f2e0b96ed7b8f7/.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: 127
  Pass (FILTER=PASS): 10 (7.9%)
  Fail (FILTER=FAIL): 117 (92.1%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high): 14
  confidence_below_min(medium<high): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 10 pass, 3 fail (total: 13)
  low: 0 pass, 84 fail (total: 84)
  medium: 0 pass, 30 fail (total: 30)
Arriba filter: 127 rows -> 10 PASS; wrote aih-tih-sc-98fc22-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-98fc22-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-98fc22-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt