Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/e841c1d85ab02f7050a6aae839984e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/e841c1d85ab02f7050a6aae839984e/.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/8b/c9ffbdd94046cbf14e75a62298e84b/659_bGc-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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 209
  Pass (FILTER=PASS): 23 (11.0%)
  Fail (FILTER=FAIL): 186 (89.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 72
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 23 pass, 4 fail (total: 27)
  low: 0 pass, 82 fail (total: 82)
  medium: 0 pass, 100 fail (total: 100)
Arriba filter: 209 rows -> 23 PASS; wrote 659_bGc-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_bGc-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt