Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/1974ce08707ea3b7ee070b8ab0eb03/aih-tih-sc-cece97-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/9e670acbb9df3aebc2f1562191a53b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/9e670acbb9df3aebc2f1562191a53b/.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-eb5d3959-7137-45a9-9f26-41f9201dcf7f/81/be38f7f47cc30e4a107d9e602cb8fb/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: 198
  Pass (FILTER=PASS): 5 (2.5%)
  Fail (FILTER=FAIL): 193 (97.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 56
  confidence_below_min(low<high): 23
  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): 20
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 7
  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): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 5 pass, 3 fail (total: 8)
  low: 0 pass, 87 fail (total: 87)
  medium: 0 pass, 103 fail (total: 103)
Arriba filter: 198 rows -> 5 PASS; wrote aih-tih-sc-cece97-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-cece97-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-cece97-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt