Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/82bb9cc5f965f64b0920c55f6a6518/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/6dfb0ff16151e59b054c779a45e0d5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/6dfb0ff16151e59b054c779a45e0d5/.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-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 239
  Pass (FILTER=PASS): 8 (3.3%)
  Fail (FILTER=FAIL): 231 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 32
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4

Breakdown by confidence:
  high: 8 pass, 9 fail (total: 17)
  low: 0 pass, 107 fail (total: 107)
  medium: 0 pass, 115 fail (total: 115)
Arriba filter: 239 rows -> 8 PASS; wrote aih-tih-sc-9fb608-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-9fb608-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt