Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/c501e57bb5539176ab38eed55f717a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/c501e57bb5539176ab38eed55f717a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/0ecb691d2fb6593b74cd02f4735100/659_bGc-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 154
  Pass (FILTER=PASS): 10 (6.5%)
  Fail (FILTER=FAIL): 144 (93.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 55
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 10 pass, 0 fail (total: 10)
  low: 0 pass, 48 fail (total: 48)
  medium: 0 pass, 96 fail (total: 96)
Arriba filter: 154 rows -> 10 PASS; wrote 659_bGc-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_bGc-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bGc-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt