Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/613bd51a79a8dd91548cc56182c611/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/444c2d50e2d9eb6dca67130a12ef9c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/444c2d50e2d9eb6dca67130a12ef9c/.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-eb5d3959-7137-45a9-9f26-41f9201dcf7f/81/be38f7f47cc30e4a107d9e602cb8fb/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: 417
  Pass (FILTER=PASS): 46 (11.0%)
  Fail (FILTER=FAIL): 371 (89.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 94
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 74
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 21
  confidence_below_min(low<high): 21
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  total_reads_below_min(5.0<8.0): 5

Breakdown by confidence:
  high: 46 pass, 13 fail (total: 59)
  low: 0 pass, 151 fail (total: 151)
  medium: 0 pass, 207 fail (total: 207)
Arriba filter: 417 rows -> 46 PASS; wrote aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt