Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/fc261d836f60fb7140be7249a1e86a/FFPE_HD789_01_RNA_13_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/8e348bf499210aa93aa226c93fb1c8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/8e348bf499210aa93aa226c93fb1c8/.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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 15 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 453
  Pass (FILTER=PASS): 62 (13.7%)
  Fail (FILTER=FAIL): 391 (86.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 15
  All 15 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 71
  confidence_below_min(medium<high): 69
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 34
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(low<high): 18
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5

Breakdown by confidence:
  high: 62 pass, 10 fail (total: 72)
  low: 0 pass, 203 fail (total: 203)
  medium: 0 pass, 178 fail (total: 178)
Arriba filter: 453 rows -> 62 PASS; wrote FFPE_HD789_01_RNA_13_B23WHTKLT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_B23WHTKLT4_1.arriba.fusions.filter_summary.txt