Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/28f26d573c4076b53daca2188e5b2f/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/b64b7e2c6e2f1cfd7e0629e0b5a883/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/b64b7e2c6e2f1cfd7e0629e0b5a883/.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-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 201
  Pass (FILTER=PASS): 26 (12.9%)
  Fail (FILTER=FAIL): 175 (87.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 73
  confidence_below_min(low<high): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0);aih_curated_blacklist: 1
  total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 26 pass, 1 fail (total: 27)
  low: 0 pass, 75 fail (total: 75)
  medium: 0 pass, 99 fail (total: 99)
Arriba filter: 201 rows -> 26 PASS; wrote aih-tih-sc-1d9134-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-1d9134-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt