Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/c9508fd5bee0d2ee34fa09eae5d607/PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/68cc5d0ade68c0b5beaee43530763b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/68cc5d0ade68c0b5beaee43530763b/.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-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 141
  Pass (FILTER=PASS): 3 (2.1%)
  Fail (FILTER=FAIL): 138 (97.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 66
  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): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high): 4
  confidence_below_min(medium<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(5.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 3 pass, 2 fail (total: 5)
  low: 0 pass, 60 fail (total: 60)
  medium: 0 pass, 76 fail (total: 76)
Arriba filter: 141 rows -> 3 PASS; wrote PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.filtered.tsv and PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.filter_summary.txt