Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/39a495e943fde2fc24b0c98dfaed30/tih_rna_sample_00457_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/ab585f375d01e4ee00299b0e775aec/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/ab585f375d01e4ee00299b0e775aec/.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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 249
  Pass (FILTER=PASS): 28 (11.2%)
  Fail (FILTER=FAIL): 221 (88.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 68
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(low<high): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 28 pass, 5 fail (total: 33)
  low: 0 pass, 88 fail (total: 88)
  medium: 0 pass, 128 fail (total: 128)
Arriba filter: 249 rows -> 28 PASS; wrote tih_rna_sample_00457_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00457_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00457_B23WHTKLT4_2.arriba.fusions.filter_summary.txt