Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/a42e38265b0c966f838f4edad9f0f4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/a42e38265b0c966f838f4edad9f0f4/.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/09/0a695689648bf554ad3a315bf71e8e/FFPE_HD789_01_RNA_13_A23WKFTLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-13dfb8f7-c999-4ef0-9260-22ba79cf647d/75/c52a23060671398a8253a658f32ecc/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 436
  Pass (FILTER=PASS): 59 (13.5%)
  Fail (FILTER=FAIL): 377 (86.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 93
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 53
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 32
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 28
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  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(7.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7

Breakdown by confidence:
  high: 59 pass, 8 fail (total: 67)
  low: 0 pass, 178 fail (total: 178)
  medium: 0 pass, 191 fail (total: 191)
Arriba filter: 436 rows -> 59 PASS; wrote FFPE_HD789_01_RNA_13_A23WKFTLT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_A23WKFTLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_A23WKFTLT4_1.arriba.fusions.filter_summary.txt