Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/d97a3c8dff78d6caeaf9b06871ff27/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/ecc4bbbad800ad5ab3fd6ee568d1e5/659_djb-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/d97a3c8dff78d6caeaf9b06871ff27/.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 247
  Pass (FILTER=PASS): 32 (13.0%)
  Fail (FILTER=FAIL): 215 (87.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 73
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 32 pass, 4 fail (total: 36)
  low: 0 pass, 112 fail (total: 112)
  medium: 0 pass, 99 fail (total: 99)
Arriba filter: 247 rows -> 32 PASS; wrote 659_djb-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_djb-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_djb-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt