Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/162538db0c81a2aab4b7902d4cbe26/tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/3b8a38cd78512cbd48a5989184933d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/3b8a38cd78512cbd48a5989184933d/.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-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 235
  Pass (FILTER=PASS): 32 (13.6%)
  Fail (FILTER=FAIL): 203 (86.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 67
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 32 pass, 13 fail (total: 45)
  low: 0 pass, 82 fail (total: 82)
  medium: 0 pass, 108 fail (total: 108)
Arriba filter: 235 rows -> 32 PASS; wrote tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.filter_summary.txt