Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/0170a80ddc17a0cad7b8eeb1d6c984/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/0170a80ddc17a0cad7b8eeb1d6c984/.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/8d/38ceaa4449e38c337a3bbec0a51fb1/659_cGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-0c31b8cc-cacb-407a-8f2b-eb2d8317e249/e8/83b3d86dc9f1df6763490ba67ef20d/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 23
  Pass (FILTER=PASS): 2 (8.7%)
  Fail (FILTER=FAIL): 21 (91.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(2.0<8.0): 1
  confidence_below_min(medium<high): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 4 fail (total: 6)
  low: 0 pass, 13 fail (total: 13)
  medium: 0 pass, 4 fail (total: 4)
Arriba filter: 23 rows -> 2 PASS; wrote 659_cGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_cGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt