Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/2e255bf0e5a13ab14c4086f92d62fd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/2e255bf0e5a13ab14c4086f92d62fd/.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/97/7b559939e9cb735dfd30098f24a5ab/aih-tih-sc-7f9674-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 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 233
  Pass (FILTER=PASS): 49 (21.0%)
  Fail (FILTER=FAIL): 184 (79.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 71
  confidence_below_min(low<high): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<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(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(6.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 49 pass, 7 fail (total: 56)
  low: 0 pass, 74 fail (total: 74)
  medium: 0 pass, 103 fail (total: 103)
Arriba filter: 233 rows -> 49 PASS; wrote aih-tih-sc-7f9674-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-7f9674-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-7f9674-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt