Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/b147bcef1ee2d114e28a89b82ed829/659_dfA-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/d6400222419fa251e974a7db111d6f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/d6400222419fa251e974a7db111d6f/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 399
  Pass (FILTER=PASS): 102 (25.6%)
  Fail (FILTER=FAIL): 297 (74.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 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): 51
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 6

Breakdown by confidence:
  high: 102 pass, 7 fail (total: 109)
  low: 0 pass, 135 fail (total: 135)
  medium: 0 pass, 155 fail (total: 155)
Arriba filter: 399 rows -> 102 PASS; wrote 659_dfA-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_dfA-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_dfA-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt