Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/d9b7ac85fea5cc5e44557061c04bbd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/d9b7ac85fea5cc5e44557061c04bbd/.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/37/5aac74134cffc41a28410f08ed2027/aih-tih-sc-6473fb-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/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: 136
  Pass (FILTER=PASS): 7 (5.1%)
  Fail (FILTER=FAIL): 129 (94.9%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 66
  confidence_below_min(low<high): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 7 pass, 3 fail (total: 10)
  low: 0 pass, 55 fail (total: 55)
  medium: 0 pass, 71 fail (total: 71)
Arriba filter: 136 rows -> 7 PASS; wrote aih-tih-sc-6473fb-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-6473fb-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-6473fb-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt