Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/ca6067c5189b5caafd65641fcfaa96/aih-tih-sc-af602e-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/fd767d78144a67d2cf5b9f67d668c1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/fd767d78144a67d2cf5b9f67d668c1/.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-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 311
  Pass (FILTER=PASS): 37 (11.9%)
  Fail (FILTER=FAIL): 274 (88.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 89
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 22
  confidence_below_min(low<high): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 37 pass, 14 fail (total: 51)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 149 fail (total: 149)
Arriba filter: 311 rows -> 37 PASS; wrote aih-tih-sc-af602e-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-af602e-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-af602e-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt