Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/b868a1212167abd12131f67bc27f00/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/b868a1212167abd12131f67bc27f00/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/716b807418dd37eb9a183afb2d742f/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.arriba.fusions.tsv
  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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 362
  Pass (FILTER=PASS): 43 (11.9%)
  Fail (FILTER=FAIL): 319 (88.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 94
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 50
  confidence_below_min(low<high): 28
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4

Breakdown by confidence:
  high: 43 pass, 3 fail (total: 46)
  low: 0 pass, 128 fail (total: 128)
  medium: 0 pass, 188 fail (total: 188)
Arriba filter: 362 rows -> 43 PASS; wrote aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt