Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/6b01b7ae0999dace801fc4fb2818f2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/6b01b7ae0999dace801fc4fb2818f2/.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/01/2b83bf11ab29068370402180372bef/aih-tih-sc-f26674-R1_A23YTGFLT4_1.arriba.fusions.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 277
  Pass (FILTER=PASS): 8 (2.9%)
  Fail (FILTER=FAIL): 269 (97.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 87
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 39
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4

Breakdown by confidence:
  high: 8 pass, 8 fail (total: 16)
  low: 0 pass, 119 fail (total: 119)
  medium: 0 pass, 142 fail (total: 142)
Arriba filter: 277 rows -> 8 PASS; wrote aih-tih-sc-f26674-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-f26674-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-f26674-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt