Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/12995386287e389f2472f6f3e1fd96/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/12995386287e389f2472f6f3e1fd96/.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/10/4e249d976f6b6512fe49a63f2097b6/tih_rna_sample_00650_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/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: 253
  Pass (FILTER=PASS): 31 (12.3%)
  Fail (FILTER=FAIL): 222 (87.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 59
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 30
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 31 pass, 8 fail (total: 39)
  low: 0 pass, 113 fail (total: 113)
  medium: 0 pass, 101 fail (total: 101)
Arriba filter: 253 rows -> 31 PASS; wrote tih_rna_sample_00650_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00650_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00650_B23MVV7LT4_1.arriba.fusions.filter_summary.txt