Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/d1b5a00eb0b9c25166f1e4682313f7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/d1b5a00eb0b9c25166f1e4682313f7/.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/21/8edd19f4d29b5222cde050c5a141b5/1173_JXL_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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 273
  Pass (FILTER=PASS): 29 (10.6%)
  Fail (FILTER=FAIL): 244 (89.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 97
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 48
  confidence_below_min(low<high): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 29 pass, 1 fail (total: 30)
  low: 0 pass, 124 fail (total: 124)
  medium: 0 pass, 119 fail (total: 119)
Arriba filter: 273 rows -> 29 PASS; wrote 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt