Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/5a3e84af3fd5d1f89b2ba72c2f1e62/659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/8c73b61309255f91a0b789cd201f62/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/8c73b61309255f91a0b789cd201f62/.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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 309
  Pass (FILTER=PASS): 39 (12.6%)
  Fail (FILTER=FAIL): 270 (87.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 84
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 20
  confidence_below_min(low<high): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 39 pass, 9 fail (total: 48)
  low: 0 pass, 117 fail (total: 117)
  medium: 0 pass, 144 fail (total: 144)
Arriba filter: 309 rows -> 39 PASS; wrote 659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt