Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/62af6f921fbc9aa2b5918f048c9884/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/9418584173443281ee2b1e944be1d4/aih-tih-sc-0a6b7b-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/62af6f921fbc9aa2b5918f048c9884/.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 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 250
  Pass (FILTER=PASS): 25 (10.0%)
  Fail (FILTER=FAIL): 225 (90.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 88
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 24
  confidence_below_min(low<high): 21
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  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(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 25 pass, 6 fail (total: 31)
  low: 0 pass, 102 fail (total: 102)
  medium: 0 pass, 117 fail (total: 117)
Arriba filter: 250 rows -> 25 PASS; wrote aih-tih-sc-0a6b7b-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-0a6b7b-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-0a6b7b-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt