Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/2182d0bbd9412b93977b25adb00167/tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/d4751b15b27853bc9cfe88919f5044/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/d4751b15b27853bc9cfe88919f5044/.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 313
  Pass (FILTER=PASS): 53 (16.9%)
  Fail (FILTER=FAIL): 260 (83.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 66
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 35
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 53 pass, 9 fail (total: 62)
  low: 0 pass, 107 fail (total: 107)
  medium: 0 pass, 144 fail (total: 144)
Arriba filter: 313 rows -> 53 PASS; wrote tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.filter_summary.txt