Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/5f3e1deabfedbbbdd9be38666e0c0d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/5f3e1deabfedbbbdd9be38666e0c0d/.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/0f/1701a08c18835ea08b996aa3502a52/FFPE_HD789_01_RNA_13_A23MVY2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 417
  Pass (FILTER=PASS): 61 (14.6%)
  Fail (FILTER=FAIL): 356 (85.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 75
  confidence_below_min(medium<high): 65
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 21
  confidence_below_min(low<high): 19
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5

Breakdown by confidence:
  high: 61 pass, 12 fail (total: 73)
  low: 0 pass, 174 fail (total: 174)
  medium: 0 pass, 170 fail (total: 170)
Arriba filter: 417 rows -> 61 PASS; wrote FFPE_HD789_01_RNA_13_A23MVY2LT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_A23MVY2LT4_1.arriba.fusions.filter_summary.txt