Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/b74f27fff42ea4adf6b994f956ac5d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/b74f27fff42ea4adf6b994f956ac5d/.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/07/1cffe8d120cdb64eaed81bfc32cc14/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-eb5d3959-7137-45a9-9f26-41f9201dcf7f/81/be38f7f47cc30e4a107d9e602cb8fb/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: 370
  Pass (FILTER=PASS): 73 (19.7%)
  Fail (FILTER=FAIL): 297 (80.3%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 103
  confidence_below_min(low<high): 27
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3

Breakdown by confidence:
  high: 73 pass, 6 fail (total: 79)
  low: 0 pass, 101 fail (total: 101)
  medium: 0 pass, 190 fail (total: 190)
Arriba filter: 370 rows -> 73 PASS; wrote aih-tih-sc-28eb14-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-28eb14-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt