Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/2ae513a2c4969f7265cdc0d268287f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/2ae513a2c4969f7265cdc0d268287f/.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/48/869fc9b128e307709d76b05e055900/FFPE_HD789_01_RNA_13_A23T55JLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fe242a7f-c5b9-4d3f-88fa-f3e739280d3a/0e/64006b836d7933c012afba79f66ebb/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: 385
  Pass (FILTER=PASS): 63 (16.4%)
  Fail (FILTER=FAIL): 322 (83.6%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 65
  confidence_below_min(medium<high): 55
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 21
  confidence_below_min(low<high): 21
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4

Breakdown by confidence:
  high: 63 pass, 6 fail (total: 69)
  low: 0 pass, 169 fail (total: 169)
  medium: 0 pass, 147 fail (total: 147)
Arriba filter: 385 rows -> 63 PASS; wrote FFPE_HD789_01_RNA_13_A23T55JLT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_A23T55JLT4_1.arriba.fusions.filter_summary.txt