Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/4e7e21271351cd402ce957db9f9825/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/4e7e21271351cd402ce957db9f9825/.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/ef/7bb9db975c1f0feaba66592b8599aa/aih-tih-sc-a9fe91-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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 211
  Pass (FILTER=PASS): 13 (6.2%)
  Fail (FILTER=FAIL): 198 (93.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 47
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 13 pass, 2 fail (total: 15)
  low: 0 pass, 93 fail (total: 93)
  medium: 0 pass, 103 fail (total: 103)
Arriba filter: 211 rows -> 13 PASS; wrote aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt