Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/3a516748e6c6f9e7853cf5e6328719/PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/7f63a893b5946b4ace25fee015cbc1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/7f63a893b5946b4ace25fee015cbc1/.command.sh
  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 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 214
  Pass (FILTER=PASS): 16 (7.5%)
  Fail (FILTER=FAIL): 198 (92.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 73
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2

Breakdown by confidence:
  high: 16 pass, 6 fail (total: 22)
  low: 0 pass, 98 fail (total: 98)
  medium: 0 pass, 94 fail (total: 94)
Arriba filter: 214 rows -> 16 PASS; wrote PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.filtered.tsv and PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.filter_summary.txt