Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/46b725fb25bf8267649ccf693675c4/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/44bc3a488194ca0a8d03d97d4ac6d7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/44bc3a488194ca0a8d03d97d4ac6d7/.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-fe242a7f-c5b9-4d3f-88fa-f3e739280d3a/0e/64006b836d7933c012afba79f66ebb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 162
  Pass (FILTER=PASS): 23 (14.2%)
  Fail (FILTER=FAIL): 139 (85.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1

Breakdown by confidence:
  high: 23 pass, 0 fail (total: 23)
  low: 0 pass, 52 fail (total: 52)
  medium: 0 pass, 87 fail (total: 87)
Arriba filter: 162 rows -> 23 PASS; wrote 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt