Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/5d5e24b851e83b7e8c7cb4c3b31dbf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/5d5e24b851e83b7e8c7cb4c3b31dbf/.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/fd/7a03603c1b7fe130287f05fdba9e95/aih-tih-sc-9b89b4-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 15 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 316
  Pass (FILTER=PASS): 36 (11.4%)
  Fail (FILTER=FAIL): 280 (88.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 15
  All 15 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 93
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 21
  confidence_below_min(low<high): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 36 pass, 5 fail (total: 41)
  low: 0 pass, 124 fail (total: 124)
  medium: 0 pass, 151 fail (total: 151)
Arriba filter: 316 rows -> 36 PASS; wrote aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt