Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/23fd7b89201a6df2bb2725015e17fa/tih_rna_sample_00721_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/3dbc980cf77ee15a55816ba452396a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/3dbc980cf77ee15a55816ba452396a/.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 16 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 367
  Pass (FILTER=PASS): 40 (10.9%)
  Fail (FILTER=FAIL): 327 (89.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 16
  All 16 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 112
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 43
  confidence_below_min(low<high): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(7.0<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: 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 40 pass, 10 fail (total: 50)
  low: 0 pass, 141 fail (total: 141)
  medium: 0 pass, 176 fail (total: 176)
Arriba filter: 367 rows -> 40 PASS; wrote tih_rna_sample_00721_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00721_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00721_B23MVV7LT4_1.arriba.fusions.filter_summary.txt