Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/5803e2ab3f1e8a893134cb906aff7e/aih-tih-sc-76a805-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/94f41bc0b00f7861d8e67af9c6fc2f/.command.sh
  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/62/94f41bc0b00f7861d8e67af9c6fc2f/.command.run
  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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 228
  Pass (FILTER=PASS): 15 (6.6%)
  Fail (FILTER=FAIL): 213 (93.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 57
  confidence_below_min(low<high): 28
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  aih_curated_blacklist: 2

Breakdown by confidence:
  high: 15 pass, 5 fail (total: 20)
  low: 0 pass, 103 fail (total: 103)
  medium: 0 pass, 105 fail (total: 105)
Arriba filter: 228 rows -> 15 PASS; wrote aih-tih-sc-76a805-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-76a805-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-76a805-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt