Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/c189fad1e05c5d9b12607cc1edb96f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/c189fad1e05c5d9b12607cc1edb96f/.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/b7/069c9de99ecbbd630f1f52eaa24641/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_2.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 65
  Pass (FILTER=PASS): 2 (3.1%)
  Fail (FILTER=FAIL): 63 (96.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(medium<high): 6
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(2.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 5 fail (total: 7)
  low: 0 pass, 43 fail (total: 43)
  medium: 0 pass, 15 fail (total: 15)
Arriba filter: 65 rows -> 2 PASS; wrote 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt