Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/d9d17cbc05f0f46bd3e444e95d1653/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/d9d17cbc05f0f46bd3e444e95d1653/.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/f2/95d84957c79e015cee90f256bf8dfb/A673_FFPE_RNA_0001_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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 275
  Pass (FILTER=PASS): 43 (15.6%)
  Fail (FILTER=FAIL): 232 (84.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 53
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 43 pass, 6 fail (total: 49)
  low: 0 pass, 109 fail (total: 109)
  medium: 0 pass, 117 fail (total: 117)
Arriba filter: 275 rows -> 43 PASS; wrote A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt