Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/b8b325cd4f7824c97a07f45f194c09/aih-tih-sc-b157e9-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/ad49f6965b7e5ea47d40858095af63/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/ad49f6965b7e5ea47d40858095af63/.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-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 316
  Pass (FILTER=PASS): 51 (16.1%)
  Fail (FILTER=FAIL): 265 (83.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 80
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 42
  confidence_below_min(low<high): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 51 pass, 12 fail (total: 63)
  low: 0 pass, 132 fail (total: 132)
  medium: 0 pass, 121 fail (total: 121)
Arriba filter: 316 rows -> 51 PASS; wrote aih-tih-sc-b157e9-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-b157e9-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-b157e9-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt