Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/b45ecaa7b51e9736bdf91bf3b3e6b2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/b45ecaa7b51e9736bdf91bf3b3e6b2/.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/71/0f18d38932ed2832306353830e1536/tih_rna_sample_00686_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 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 222
  Pass (FILTER=PASS): 6 (2.7%)
  Fail (FILTER=FAIL): 216 (97.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 89
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 3
  confidence_below_min(low<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 6 pass, 4 fail (total: 10)
  low: 0 pass, 77 fail (total: 77)
  medium: 0 pass, 135 fail (total: 135)
Arriba filter: 222 rows -> 6 PASS; wrote tih_rna_sample_00686_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00686_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00686_B23MVV7LT4_1.arriba.fusions.filter_summary.txt