Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/55cb0678ae84e9ac83ca2367c55c5a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/727ca35bc68d2598d342c60543b214/659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/55cb0678ae84e9ac83ca2367c55c5a/.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-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: 201
  Pass (FILTER=PASS): 8 (4.0%)
  Fail (FILTER=FAIL): 193 (96.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 98
  confidence_below_min(low<high): 18
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 8 pass, 0 fail (total: 8)
  low: 0 pass, 77 fail (total: 77)
  medium: 0 pass, 116 fail (total: 116)
Arriba filter: 201 rows -> 8 PASS; wrote 659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt