Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/20406ba9bf5958ca5526a988ad4ed3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/20406ba9bf5958ca5526a988ad4ed3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/419bcfc975b5043fa7fe776c121b46/FFPE_HD789_01_RNA_13_B23WHYVLT4_1.arriba.fusions.tsv
  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-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/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: 391
  Pass (FILTER=PASS): 58 (14.8%)
  Fail (FILTER=FAIL): 333 (85.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 60
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 58
  confidence_below_min(low<high): 39
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 28
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5

Breakdown by confidence:
  high: 58 pass, 8 fail (total: 66)
  low: 0 pass, 178 fail (total: 178)
  medium: 0 pass, 147 fail (total: 147)
Arriba filter: 391 rows -> 58 PASS; wrote FFPE_HD789_01_RNA_13_B23WHYVLT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_B23WHYVLT4_1.arriba.fusions.filter_summary.txt