Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/30abae0b74ac86c4ffbcc7885bf378/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/30abae0b74ac86c4ffbcc7885bf378/.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/10/bc875b76717e06d9795e16037df377/BVT_FFPE_TRNA_stm_08_A23WKFTLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-13dfb8f7-c999-4ef0-9260-22ba79cf647d/75/c52a23060671398a8253a658f32ecc/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 62
  Pass (FILTER=PASS): 5 (8.1%)
  Fail (FILTER=FAIL): 57 (91.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 11
  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): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 5 pass, 2 fail (total: 7)
  low: 0 pass, 25 fail (total: 25)
  medium: 0 pass, 30 fail (total: 30)
Arriba filter: 62 rows -> 5 PASS; wrote BVT_FFPE_TRNA_stm_08_A23WKFTLT4_2.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_stm_08_A23WKFTLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_stm_08_A23WKFTLT4_2.arriba.fusions.filter_summary.txt