Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/f6cfc4d8dcc172f16a89ed9c16d654/659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/e32dfe28eac3e5628475efa441c7bf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/e32dfe28eac3e5628475efa441c7bf/.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 120
  Pass (FILTER=PASS): 4 (3.3%)
  Fail (FILTER=FAIL): 116 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high): 4
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 2 fail (total: 6)
  low: 0 pass, 42 fail (total: 42)
  medium: 0 pass, 72 fail (total: 72)
Arriba filter: 120 rows -> 4 PASS; wrote 659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt