Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/59a65444c624a858ca588051ae4dab/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/59a65444c624a858ca588051ae4dab/.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/96/c33cf11d90d7a6eeb301fc38f7a869/aih-tih-sc-da06ce-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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 195
  Pass (FILTER=PASS): 8 (4.1%)
  Fail (FILTER=FAIL): 187 (95.9%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 54
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 8 pass, 1 fail (total: 9)
  low: 0 pass, 89 fail (total: 89)
  medium: 0 pass, 97 fail (total: 97)
Arriba filter: 195 rows -> 8 PASS; wrote aih-tih-sc-da06ce-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-da06ce-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-da06ce-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt