Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/58b2798f662ea1cd31401b4c08821a/tih_rna_sample_00090_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/d94b41cb3e2a94937b021c5e664b88/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/d94b41cb3e2a94937b021c5e664b88/.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 49
  Pass (FILTER=PASS): 3 (6.1%)
  Fail (FILTER=FAIL): 46 (93.9%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(medium<high): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<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
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 3 pass, 1 fail (total: 4)
  low: 0 pass, 37 fail (total: 37)
  medium: 0 pass, 8 fail (total: 8)
Arriba filter: 49 rows -> 3 PASS; wrote tih_rna_sample_00090_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00090_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00090_B23WHTKLT4_1.arriba.fusions.filter_summary.txt