Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/d422621f9135894e301a0bbab77e6b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/d422621f9135894e301a0bbab77e6b/.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/ff/40439eaa14ccc982191f927ca85459/tih_rna_sample_00737_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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 310
  Pass (FILTER=PASS): 27 (8.7%)
  Fail (FILTER=FAIL): 283 (91.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 83
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 54
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 32
  confidence_below_min(low<high): 22
  confidence_below_min(low<high);total_reads_below_min(3.0<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(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 27 pass, 4 fail (total: 31)
  low: 0 pass, 152 fail (total: 152)
  medium: 0 pass, 127 fail (total: 127)
Arriba filter: 310 rows -> 27 PASS; wrote tih_rna_sample_00737_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00737_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00737_B23MVV7LT4_1.arriba.fusions.filter_summary.txt