Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/5310649a0b15fcadb5b9228c62b38b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/5310649a0b15fcadb5b9228c62b38b/.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/a8/fee4f5f73ac63e45927738f3081699/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.arriba.fusions.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 243
  Pass (FILTER=PASS): 9 (3.7%)
  Fail (FILTER=FAIL): 234 (96.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 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): 30
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(low<high): 16
  confidence_below_min(medium<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(low<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<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(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  aih_curated_blacklist: 2

Breakdown by confidence:
  high: 9 pass, 4 fail (total: 13)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 119 fail (total: 119)
Arriba filter: 243 rows -> 9 PASS; wrote aih-tih-sc-01eb49-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-01eb49-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-01eb49-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt