Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/a74cc5714ead2eec9a10335ec0310f/659_Lx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/dbeb4cbd0d20aa5b991469f2b7c881/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/dbeb4cbd0d20aa5b991469f2b7c881/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 185
  Pass (FILTER=PASS): 18 (9.7%)
  Fail (FILTER=FAIL): 167 (90.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 80
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 18 pass, 1 fail (total: 19)
  low: 0 pass, 66 fail (total: 66)
  medium: 0 pass, 100 fail (total: 100)
Arriba filter: 185 rows -> 18 PASS; wrote 659_Lx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_Lx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_Lx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt