Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/175ddf6bf16419d03daff01656dd46/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/ad3d51e13cc042b18388f88e0e4e12/FFPE_V4_0002_RNA_0006_A23MVY2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/175ddf6bf16419d03daff01656dd46/.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-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 153
  Pass (FILTER=PASS): 21 (13.7%)
  Fail (FILTER=FAIL): 132 (86.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 25
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  aih_curated_blacklist: 1
  total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 21 pass, 5 fail (total: 26)
  low: 0 pass, 83 fail (total: 83)
  medium: 0 pass, 44 fail (total: 44)
Arriba filter: 153 rows -> 21 PASS; wrote FFPE_V4_0002_RNA_0006_A23MVY2LT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0002_RNA_0006_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0002_RNA_0006_A23MVY2LT4_1.arriba.fusions.filter_summary.txt