Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/8955789c790ec4d71e79f018e1b981/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/8955789c790ec4d71e79f018e1b981/.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/3d/52451f36d3e2290c71561b7301ee1a/659_bQZ-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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 226
  Pass (FILTER=PASS): 10 (4.4%)
  Fail (FILTER=FAIL): 216 (95.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 60
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 31
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4

Breakdown by confidence:
  high: 10 pass, 4 fail (total: 14)
  low: 0 pass, 95 fail (total: 95)
  medium: 0 pass, 117 fail (total: 117)
Arriba filter: 226 rows -> 10 PASS; wrote 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt