Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/33e96dd8d25448f1c9d8ca0680178e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/19d71552a88124b1647665db1d60dc/aih-tih-sc-3a9c1f-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/33e96dd8d25448f1c9d8ca0680178e/.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 70
  Pass (FILTER=PASS): 2 (2.9%)
  Fail (FILTER=FAIL): 68 (97.1%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(6.0<8.0);aih_curated_blacklist: 1
  total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 3 fail (total: 5)
  low: 0 pass, 46 fail (total: 46)
  medium: 0 pass, 19 fail (total: 19)
Arriba filter: 70 rows -> 2 PASS; wrote aih-tih-sc-3a9c1f-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-3a9c1f-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-3a9c1f-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt