Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/17aead46e2a8fca692d198b7088069/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/17aead46e2a8fca692d198b7088069/.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/fe/160ac45f3167329bfb82fb99f09df7/659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 37
  Pass (FILTER=PASS): 3 (8.1%)
  Fail (FILTER=FAIL): 34 (91.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high): 2
  confidence_below_min(medium<high): 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
  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(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1

Breakdown by confidence:
  high: 3 pass, 0 fail (total: 3)
  low: 0 pass, 22 fail (total: 22)
  medium: 0 pass, 12 fail (total: 12)
Arriba filter: 37 rows -> 3 PASS; wrote 659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt