Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/3010e26289b7bd84dc545845220a4c/659_rd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/7e0f75efc9ffa194f9035b04f6e8ab/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/7e0f75efc9ffa194f9035b04f6e8ab/.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: 266
  Pass (FILTER=PASS): 30 (11.3%)
  Fail (FILTER=FAIL): 236 (88.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 56
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 28
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  total_reads_below_min(4.0<8.0): 3

Breakdown by confidence:
  high: 30 pass, 6 fail (total: 36)
  low: 0 pass, 135 fail (total: 135)
  medium: 0 pass, 95 fail (total: 95)
Arriba filter: 266 rows -> 30 PASS; wrote 659_rd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_rd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_rd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt