Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/e092a8656c4c4dd601d33ec103f248/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/e092a8656c4c4dd601d33ec103f248/.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/9a/04c75848c97663bcb9b28196779bfc/659_dES-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 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 416
  Pass (FILTER=PASS): 50 (12.0%)
  Fail (FILTER=FAIL): 366 (88.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 84
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 82
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  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): 6

Breakdown by confidence:
  high: 50 pass, 3 fail (total: 53)
  low: 0 pass, 186 fail (total: 186)
  medium: 0 pass, 177 fail (total: 177)
Arriba filter: 416 rows -> 50 PASS; wrote 659_dES-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_dES-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_dES-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt