Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/c45fce16b72bb58ac6c716d7add3ed/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/c45fce16b72bb58ac6c716d7add3ed/.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/29/fe575e1bf7d8b487728e992d5ee2f3/RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 204
  Pass (FILTER=PASS): 16 (7.8%)
  Fail (FILTER=FAIL): 188 (92.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 39
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 16 pass, 3 fail (total: 19)
  low: 0 pass, 99 fail (total: 99)
  medium: 0 pass, 86 fail (total: 86)
Arriba filter: 204 rows -> 16 PASS; wrote RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt