Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/c2f01c048229a4fb9c1ced76659251/tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/757d621ef433d721f2a62b311ef28b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/757d621ef433d721f2a62b311ef28b/.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 188
  Pass (FILTER=PASS): 20 (10.6%)
  Fail (FILTER=FAIL): 168 (89.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 34
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(6.0<8.0): 2
  total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2

Breakdown by confidence:
  high: 20 pass, 9 fail (total: 29)
  low: 0 pass, 78 fail (total: 78)
  medium: 0 pass, 81 fail (total: 81)
Arriba filter: 188 rows -> 20 PASS; wrote tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.filter_summary.txt