Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/ec8803ebb5bd7d5e1e2aaa245031a9/tih_rna_sample_00479_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/8681c891bef597250ab9d88f6be8e0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/8681c891bef597250ab9d88f6be8e0/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 474
  Pass (FILTER=PASS): 86 (18.1%)
  Fail (FILTER=FAIL): 388 (81.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 72
  confidence_below_min(medium<high): 65
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 38
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  total_reads_below_min(3.0<8.0): 6
  total_reads_below_min(4.0<8.0): 6

Breakdown by confidence:
  high: 86 pass, 18 fail (total: 104)
  low: 0 pass, 175 fail (total: 175)
  medium: 0 pass, 195 fail (total: 195)
Arriba filter: 474 rows -> 86 PASS; wrote tih_rna_sample_00479_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00479_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00479_B23WHTKLT4_2.arriba.fusions.filter_summary.txt