Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/7891bce182a088105723b58f4ee52a/659_ecd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/44a42fee3510f1697daaa6e5d46fc9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/44a42fee3510f1697daaa6e5d46fc9/.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-0c31b8cc-cacb-407a-8f2b-eb2d8317e249/e8/83b3d86dc9f1df6763490ba67ef20d/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 595
  Pass (FILTER=PASS): 77 (12.9%)
  Fail (FILTER=FAIL): 518 (87.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 161
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 88
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 41
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 23
  confidence_below_min(low<high): 23
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7

Breakdown by confidence:
  high: 77 pass, 15 fail (total: 92)
  low: 0 pass, 227 fail (total: 227)
  medium: 0 pass, 276 fail (total: 276)
Arriba filter: 595 rows -> 77 PASS; wrote 659_ecd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_ecd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_ecd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt