Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/baeed0f3446f48da98b008d0e0f320/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/baeed0f3446f48da98b008d0e0f320/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/38e09d1a3a39b9e833484a1501a447/tih_rna_sample_00704_B23MVV7LT4_1.arriba.fusions.tsv
  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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 334
  Pass (FILTER=PASS): 32 (9.6%)
  Fail (FILTER=FAIL): 302 (90.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 82
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 49
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 29
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(low<high): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 32 pass, 3 fail (total: 35)
  low: 0 pass, 154 fail (total: 154)
  medium: 0 pass, 145 fail (total: 145)
Arriba filter: 334 rows -> 32 PASS; wrote tih_rna_sample_00704_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00704_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00704_B23MVV7LT4_1.arriba.fusions.filter_summary.txt