Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/727a1e178c17a9a1ef41593c883d3a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/727a1e178c17a9a1ef41593c883d3a/.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/80/c8fa64440996f761695b2bda581b2a/SW780_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-6ef41cd9-2e18-4687-842c-3f6f49c5643f/f2/edcdb43d4676ed2a5254ed1bf31faa/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 383
  Pass (FILTER=PASS): 71 (18.5%)
  Fail (FILTER=FAIL): 312 (81.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 65
  confidence_below_min(medium<high): 50
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 20
  confidence_below_min(low<high): 17
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5

Breakdown by confidence:
  high: 71 pass, 7 fail (total: 78)
  low: 0 pass, 175 fail (total: 175)
  medium: 0 pass, 130 fail (total: 130)
Arriba filter: 383 rows -> 71 PASS; wrote SW780_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered.tsv and SW780_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: SW780_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filter_summary.txt