Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/3025f6c5d6b82f29d012aa3f13f572/aih-tih-sc-5d3207-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/4b497a2aeaaca2db2bcf23d094dfc4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/4b497a2aeaaca2db2bcf23d094dfc4/.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-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 191
  Pass (FILTER=PASS): 58 (30.4%)
  Fail (FILTER=FAIL): 133 (69.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 47
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 58 pass, 1 fail (total: 59)
  low: 0 pass, 61 fail (total: 61)
  medium: 0 pass, 71 fail (total: 71)
Arriba filter: 191 rows -> 58 PASS; wrote aih-tih-sc-5d3207-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-5d3207-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-5d3207-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt