Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/15205c02f5de0551d50e613474f567/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/15205c02f5de0551d50e613474f567/.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/45/6c23d6e96addcbd7a38a6f4830b8d6/aih-tih-sc-5ceb9a-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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 298
  Pass (FILTER=PASS): 84 (28.2%)
  Fail (FILTER=FAIL): 214 (71.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 43
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 40
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(low<high): 15
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 84 pass, 2 fail (total: 86)
  low: 0 pass, 119 fail (total: 119)
  medium: 0 pass, 93 fail (total: 93)
Arriba filter: 298 rows -> 84 PASS; wrote aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt