Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/c7de25be1778ffe69227fc6374510f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/c7de25be1778ffe69227fc6374510f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/056f1e495c471b5005266df47975b8/tih_rna_sample_00163_B23WHTKLT4_1.arriba.fusions.tsv
  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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 192
  Pass (FILTER=PASS): 15 (7.8%)
  Fail (FILTER=FAIL): 177 (92.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 62
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 14
  confidence_below_min(medium<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(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 15 pass, 10 fail (total: 25)
  low: 0 pass, 61 fail (total: 61)
  medium: 0 pass, 106 fail (total: 106)
Arriba filter: 192 rows -> 15 PASS; wrote tih_rna_sample_00163_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00163_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00163_B23WHTKLT4_1.arriba.fusions.filter_summary.txt