Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/c75b39cbf0600b55488f0a45036fcb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/c75b39cbf0600b55488f0a45036fcb/.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/55/3ab5ab3b2e4b96325517b7a6013e3c/FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 161
  Pass (FILTER=PASS): 20 (12.4%)
  Fail (FILTER=FAIL): 141 (87.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(medium<high): 18
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 20 pass, 2 fail (total: 22)
  low: 0 pass, 96 fail (total: 96)
  medium: 0 pass, 43 fail (total: 43)
Arriba filter: 161 rows -> 20 PASS; wrote FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.arriba.fusions.filter_summary.txt