Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/3e16db4eefa4b154dbb5bccd378f76/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/3e16db4eefa4b154dbb5bccd378f76/.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/ff/5a3af91497bd009ad61615a05b022c/659_end-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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 351
  Pass (FILTER=PASS): 72 (20.5%)
  Fail (FILTER=FAIL): 279 (79.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 90
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 61
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 72 pass, 5 fail (total: 77)
  low: 0 pass, 130 fail (total: 130)
  medium: 0 pass, 144 fail (total: 144)
Arriba filter: 351 rows -> 72 PASS; wrote 659_end-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_end-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_end-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt