Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/f07850033c875a85adbebdd863c7f3/tih_rna_sample_00569_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/2c3cbe12ba5d4e8499f2e5889e6ae2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/2c3cbe12ba5d4e8499f2e5889e6ae2/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 278
  Pass (FILTER=PASS): 28 (10.1%)
  Fail (FILTER=FAIL): 250 (89.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 85
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 32
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 29
  confidence_below_min(low<high): 21
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<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): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 28 pass, 4 fail (total: 32)
  low: 0 pass, 97 fail (total: 97)
  medium: 0 pass, 149 fail (total: 149)
Arriba filter: 278 rows -> 28 PASS; wrote tih_rna_sample_00569_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00569_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00569_B23MVV7LT4_1.arriba.fusions.filter_summary.txt