Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/ef615b90f3d63d681c746648e3a69a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/ef615b90f3d63d681c746648e3a69a/.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/e5/808aa1b09e177997febb1f2f032083/tih_rna_sample_00602_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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 189
  Pass (FILTER=PASS): 10 (5.3%)
  Fail (FILTER=FAIL): 179 (94.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 53
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 17
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  aih_curated_blacklist: 2

Breakdown by confidence:
  high: 10 pass, 3 fail (total: 13)
  low: 0 pass, 88 fail (total: 88)
  medium: 0 pass, 88 fail (total: 88)
Arriba filter: 189 rows -> 10 PASS; wrote tih_rna_sample_00602_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00602_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00602_B23MVV7LT4_1.arriba.fusions.filter_summary.txt