Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/bbb177da2c3f598e41e1b40d865d4f/aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/6fb17b4e83836eea677477eb49e360/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/6fb17b4e83836eea677477eb49e360/.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-e543dae6-5fea-4720-bfb6-150bf1ff20d4/33/a04540cea7c8abc13163bc03b147d5/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 110
  Pass (FILTER=PASS): 27 (24.5%)
  Fail (FILTER=FAIL): 83 (75.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 27 pass, 9 fail (total: 36)
  low: 0 pass, 43 fail (total: 43)
  medium: 0 pass, 31 fail (total: 31)
Arriba filter: 110 rows -> 27 PASS; wrote aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt