Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/491d16627e878ed6a8c41dffaf4c5c/FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/215d4bcb6b1e679eccd653846f60bf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/215d4bcb6b1e679eccd653846f60bf/.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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 162
  Pass (FILTER=PASS): 19 (11.7%)
  Fail (FILTER=FAIL): 143 (88.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high): 18
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(medium<high): 13
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  aih_curated_blacklist: 1
  total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 19 pass, 4 fail (total: 23)
  low: 0 pass, 104 fail (total: 104)
  medium: 0 pass, 35 fail (total: 35)
Arriba filter: 162 rows -> 19 PASS; wrote FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.filter_summary.txt