Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/2d8a04730e25995762d8a86906a29d/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/cd51a8175911aa1ecb8bca773d490a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/cd51a8175911aa1ecb8bca773d490a/.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 126
  Pass (FILTER=PASS): 5 (4.0%)
  Fail (FILTER=FAIL): 121 (96.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 21
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 20
  confidence_below_min(low<high): 17
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 5 pass, 3 fail (total: 8)
  low: 0 pass, 51 fail (total: 51)
  medium: 0 pass, 67 fail (total: 67)
Arriba filter: 126 rows -> 5 PASS; wrote 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt