Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/8c83f89019dbf9e5204527a3fc46f3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/8c83f89019dbf9e5204527a3fc46f3/.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/d5/4fe5db04186fa11f2747376308dedc/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.arriba.fusions.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 267
  Pass (FILTER=PASS): 32 (12.0%)
  Fail (FILTER=FAIL): 235 (88.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 55
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 39
  confidence_below_min(low<high): 27
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 32 pass, 8 fail (total: 40)
  low: 0 pass, 130 fail (total: 130)
  medium: 0 pass, 97 fail (total: 97)
Arriba filter: 267 rows -> 32 PASS; wrote aih-tih-sc-3376ed-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-3376ed-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt