Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/28c16281327d84ef0eb579e7d85aa9/tih_rna_sample_00639_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/718fe66ed4715318c435c3ee6fb562/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/718fe66ed4715318c435c3ee6fb562/.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 191
  Pass (FILTER=PASS): 34 (17.8%)
  Fail (FILTER=FAIL): 157 (82.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 22
  confidence_below_min(medium<high): 21
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 34 pass, 2 fail (total: 36)
  low: 0 pass, 96 fail (total: 96)
  medium: 0 pass, 59 fail (total: 59)
Arriba filter: 191 rows -> 34 PASS; wrote tih_rna_sample_00639_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00639_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00639_B23MVV7LT4_1.arriba.fusions.filter_summary.txt