Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/e01707cd088a1d4a9561610e48cde2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/e01707cd088a1d4a9561610e48cde2/.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/84/9bb078530a431bd412ee8585b326f1/659_cRB-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 127
  Pass (FILTER=PASS): 8 (6.3%)
  Fail (FILTER=FAIL): 119 (93.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 39
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  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): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(4.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 8 pass, 3 fail (total: 11)
  low: 0 pass, 48 fail (total: 48)
  medium: 0 pass, 68 fail (total: 68)
Arriba filter: 127 rows -> 8 PASS; wrote 659_cRB-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_cRB-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cRB-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt