Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/c950b2e102b92092512740b4a8e5ac/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/41f5426e607b9a88a301828d938e11/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/41f5426e607b9a88a301828d938e11/.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-6ef41cd9-2e18-4687-842c-3f6f49c5643f/f2/edcdb43d4676ed2a5254ed1bf31faa/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 300
  Pass (FILTER=PASS): 67 (22.3%)
  Fail (FILTER=FAIL): 233 (77.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 75
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high): 15
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 67 pass, 7 fail (total: 74)
  low: 0 pass, 104 fail (total: 104)
  medium: 0 pass, 122 fail (total: 122)
Arriba filter: 300 rows -> 67 PASS; wrote NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt