Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/a65a0299869a1ad7c565fc5c2b9f89/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/5f18dfe8ab42d7a8613f3dc29fde89/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/5f18dfe8ab42d7a8613f3dc29fde89/.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-eb5d3959-7137-45a9-9f26-41f9201dcf7f/81/be38f7f47cc30e4a107d9e602cb8fb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 204
  Pass (FILTER=PASS): 17 (8.3%)
  Fail (FILTER=FAIL): 187 (91.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 60
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(7.0<8.0): 1

Breakdown by confidence:
  high: 17 pass, 3 fail (total: 20)
  low: 0 pass, 91 fail (total: 91)
  medium: 0 pass, 93 fail (total: 93)
Arriba filter: 204 rows -> 17 PASS; wrote aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt