Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/e8d2dd6cbe2498367b8f868da8ec56/tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/b0402b7184dc5d36c51894e3f4d9b1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/b0402b7184dc5d36c51894e3f4d9b1/.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-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 119
  Pass (FILTER=PASS): 11 (9.2%)
  Fail (FILTER=FAIL): 108 (90.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 26
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high): 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: 11 pass, 2 fail (total: 13)
  low: 0 pass, 32 fail (total: 32)
  medium: 0 pass, 74 fail (total: 74)
Arriba filter: 119 rows -> 11 PASS; wrote tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.filter_summary.txt