Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/1a4aae894a0945a379e89b672ba2a6/.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/05/1a4aae894a0945a379e89b672ba2a6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/2a1c17fe35bc63ce610e60526e189d/tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 155
  Pass (FILTER=PASS): 17 (11.0%)
  Fail (FILTER=FAIL): 138 (89.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 17 pass, 2 fail (total: 19)
  low: 0 pass, 47 fail (total: 47)
  medium: 0 pass, 89 fail (total: 89)
Arriba filter: 155 rows -> 17 PASS; wrote tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.filter_summary.txt