Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/81c918fce55d461b1c6646ba5fd147/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/81c918fce55d461b1c6646ba5fd147/.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/2a/47140b67f5d3747ff4ef21a3afb6fa/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-40cc52c0-5bec-40b6-b04d-c64c51f55eff/cf/a844d18c3db3aeda7471fb3d005c4f/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 264
  Pass (FILTER=PASS): 39 (14.8%)
  Fail (FILTER=FAIL): 225 (85.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 67
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 39 pass, 2 fail (total: 41)
  low: 0 pass, 97 fail (total: 97)
  medium: 0 pass, 126 fail (total: 126)
Arriba filter: 264 rows -> 39 PASS; wrote 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt