Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/f88704ae170e9f69d7df88491dcc74/aih-tih-sc-8b9375-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/1cdcbe94562931c95c65a45cf1f20e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/1cdcbe94562931c95c65a45cf1f20e/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 664
  Pass (FILTER=PASS): 91 (13.7%)
  Fail (FILTER=FAIL): 573 (86.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 166
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 113
  confidence_below_min(low<high): 48
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 33
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5

Breakdown by confidence:
  high: 91 pass, 11 fail (total: 102)
  low: 0 pass, 310 fail (total: 310)
  medium: 0 pass, 252 fail (total: 252)
Arriba filter: 664 rows -> 91 PASS; wrote aih-tih-sc-8b9375-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-8b9375-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-8b9375-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt