Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/4ad9d72b8bba1b0ee7a83a43383ec3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/4ad9d72b8bba1b0ee7a83a43383ec3/.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/bd/19ee6dc554307a190ccd6531c0aa3d/tih_rna_sample_00146_B23WHTKLT4_1.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 264
  Pass (FILTER=PASS): 14 (5.3%)
  Fail (FILTER=FAIL): 250 (94.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 81
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 39
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 28
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 14 pass, 3 fail (total: 17)
  low: 0 pass, 123 fail (total: 123)
  medium: 0 pass, 124 fail (total: 124)
Arriba filter: 264 rows -> 14 PASS; wrote tih_rna_sample_00146_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00146_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00146_B23WHTKLT4_1.arriba.fusions.filter_summary.txt