Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/2888747a711e7cd9a14ad294ab8bf0/659_bhK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/399597928e6223c6de0f669d885e25/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/399597928e6223c6de0f669d885e25/.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 223
  Pass (FILTER=PASS): 20 (9.0%)
  Fail (FILTER=FAIL): 203 (91.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 79
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 20 pass, 1 fail (total: 21)
  low: 0 pass, 89 fail (total: 89)
  medium: 0 pass, 113 fail (total: 113)
Arriba filter: 223 rows -> 20 PASS; wrote 659_bhK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_bhK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt