Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/c53b76cf7b8b95ecb380f16e05e838/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/c53b76cf7b8b95ecb380f16e05e838/.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/d0/e0c534e5daa65f995c4e5b1072d073/HeadNeckN_FFPE_L08_RNA_01_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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 84
  Pass (FILTER=PASS): 1 (1.2%)
  Fail (FILTER=FAIL): 83 (98.8%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 31
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 1 fail (total: 2)
  low: 0 pass, 15 fail (total: 15)
  medium: 0 pass, 67 fail (total: 67)
Arriba filter: 84 rows -> 1 PASS; wrote HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered.tsv and HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.filter_summary.txt