Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/d051c239568363029e8ad483c209e9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/764fb3d708fac49b24a3b688e34fd9/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/d051c239568363029e8ad483c209e9/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 187
  Pass (FILTER=PASS): 27 (14.4%)
  Fail (FILTER=FAIL): 160 (85.6%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 29
  confidence_below_min(medium<high): 24
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<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(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 27 pass, 2 fail (total: 29)
  low: 0 pass, 96 fail (total: 96)
  medium: 0 pass, 62 fail (total: 62)
Arriba filter: 187 rows -> 27 PASS; wrote KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.arriba.fusions.filtered.tsv and KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.arriba.fusions.filter_summary.txt