Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/2750d65923e45810208543e1ce5cff/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/7d4a32f4cfb232c9cb7d2cbc2863a0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/7d4a32f4cfb232c9cb7d2cbc2863a0/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 205
  Pass (FILTER=PASS): 17 (8.3%)
  Fail (FILTER=FAIL): 188 (91.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 64
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  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): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high): 9
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2

Breakdown by confidence:
  high: 17 pass, 5 fail (total: 22)
  low: 0 pass, 88 fail (total: 88)
  medium: 0 pass, 95 fail (total: 95)
Arriba filter: 205 rows -> 17 PASS; wrote 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt