Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/e0bd95091e1495263ee98856adf406/LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/7a843ee874690db4e7f957b968de66/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/7a843ee874690db4e7f957b968de66/.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-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 108
  Pass (FILTER=PASS): 3 (2.8%)
  Fail (FILTER=FAIL): 105 (97.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 33
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 3 pass, 0 fail (total: 3)
  low: 0 pass, 27 fail (total: 27)
  medium: 0 pass, 78 fail (total: 78)
Arriba filter: 108 rows -> 3 PASS; wrote LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered.tsv and LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.filter_summary.txt