Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/13b7b6702126358229ebae06ee1d72/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/170e5de4a679a881d9c00f97b57257/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/13b7b6702126358229ebae06ee1d72/.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-fe242a7f-c5b9-4d3f-88fa-f3e739280d3a/0e/64006b836d7933c012afba79f66ebb/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: 581
  Pass (FILTER=PASS): 21 (3.6%)
  Fail (FILTER=FAIL): 560 (96.4%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 170
  confidence_below_min(medium<high): 83
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 42
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 35
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 31
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 28
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 22
  confidence_below_min(low<high): 18
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6

Breakdown by confidence:
  high: 21 pass, 8 fail (total: 29)
  low: 0 pass, 321 fail (total: 321)
  medium: 0 pass, 231 fail (total: 231)
Arriba filter: 581 rows -> 21 PASS; wrote 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt