Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/e63a2882f2ea819d45f93112ec3150/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/e63a2882f2ea819d45f93112ec3150/.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/eb/2a590e394f354fc3498d1d41cffe81/MCF7_FFPE_RNA_0001_B23LG7FLT4_1.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 762
  Pass (FILTER=PASS): 152 (19.9%)
  Fail (FILTER=FAIL): 610 (80.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 155
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 101
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 34
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 32
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 30
  confidence_below_min(low<high): 30
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 30
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 29
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 8

Breakdown by confidence:
  high: 152 pass, 14 fail (total: 166)
  low: 0 pass, 258 fail (total: 258)
  medium: 0 pass, 338 fail (total: 338)
Arriba filter: 762 rows -> 152 PASS; wrote MCF7_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and MCF7_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: MCF7_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt