Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/86de2c2e528f6ca4622c97e3d5b31f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/86de2c2e528f6ca4622c97e3d5b31f/.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/22/14357494ee1b41dc8236fa72d1eb86/1173_CI9_T1_RNA_SLD_01_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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 112
  Pass (FILTER=PASS): 4 (3.6%)
  Fail (FILTER=FAIL): 108 (96.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 27
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 15
  confidence_below_min(low<high): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  aih_curated_blacklist: 1
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 4 fail (total: 8)
  low: 0 pass, 56 fail (total: 56)
  medium: 0 pass, 48 fail (total: 48)
Arriba filter: 112 rows -> 4 PASS; wrote 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered.tsv and 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filter_summary.txt