Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3281710b7fb1cccd73cc837ff5f761/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/af1016a4e61f8156dc028518df27ca/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/af1016a4e61f8156dc028518df27ca/.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-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 216
  Pass (FILTER=PASS): 26 (12.0%)
  Fail (FILTER=FAIL): 190 (88.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 37
  confidence_below_min(medium<high): 28
  confidence_below_min(low<high): 21
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<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(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 26 pass, 2 fail (total: 28)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 77 fail (total: 77)
Arriba filter: 216 rows -> 26 PASS; wrote KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.filtered.tsv and KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.filter_summary.txt