Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/e638afdeedfa3ab6163c5b607ef478/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/e638afdeedfa3ab6163c5b607ef478/.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/cc/af94c9935d638784cf6fcf043f63f5/tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 235
  Pass (FILTER=PASS): 18 (7.7%)
  Fail (FILTER=FAIL): 217 (92.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 43
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 33
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 17
  confidence_below_min(low<high): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  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(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 18 pass, 5 fail (total: 23)
  low: 0 pass, 99 fail (total: 99)
  medium: 0 pass, 113 fail (total: 113)
Arriba filter: 235 rows -> 18 PASS; wrote tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.filter_summary.txt