Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/55af9d17c7b420eeb3c32ef901fdd3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/55af9d17c7b420eeb3c32ef901fdd3/.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/9e/2bd3f815e34fbccd150de02f04f55b/659_gK-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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 204
  Pass (FILTER=PASS): 15 (7.4%)
  Fail (FILTER=FAIL): 189 (92.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 41
  confidence_below_min(medium<high): 28
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<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
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4

Breakdown by confidence:
  high: 15 pass, 3 fail (total: 18)
  low: 0 pass, 109 fail (total: 109)
  medium: 0 pass, 77 fail (total: 77)
Arriba filter: 204 rows -> 15 PASS; wrote 659_gK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_gK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_gK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt