Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/e3a571a57d7f841f4942ce71aa6d5d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/e3a571a57d7f841f4942ce71aa6d5d/.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/27/953562a819bd6ae2e2179cfbd14885/aih-tih-sc-f4e5c4-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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 77
  Pass (FILTER=PASS): 11 (14.3%)
  Fail (FILTER=FAIL): 66 (85.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 11 pass, 6 fail (total: 17)
  low: 0 pass, 40 fail (total: 40)
  medium: 0 pass, 20 fail (total: 20)
Arriba filter: 77 rows -> 11 PASS; wrote aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt