Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/581eafc1d76af65584436c5ebf8be0/tih_rna_sample_00628_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/8afd1d7a7e1359743896df2d716be7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/8afd1d7a7e1359743896df2d716be7/.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-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 242
  Pass (FILTER=PASS): 35 (14.5%)
  Fail (FILTER=FAIL): 207 (85.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 86
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);aih_curated_blacklist: 2
  aih_curated_blacklist: 1
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 35 pass, 2 fail (total: 37)
  low: 0 pass, 93 fail (total: 93)
  medium: 0 pass, 112 fail (total: 112)
Arriba filter: 242 rows -> 35 PASS; wrote tih_rna_sample_00628_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00628_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00628_B23MVV7LT4_1.arriba.fusions.filter_summary.txt