Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/7315d42abe9a49b80f6af2242b303c/tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/d43471355cf3ab845a0a81affece32/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/d43471355cf3ab845a0a81affece32/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 55
  Pass (FILTER=PASS): 2 (3.6%)
  Fail (FILTER=FAIL): 53 (96.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(medium<high): 7
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 1 fail (total: 3)
  low: 0 pass, 33 fail (total: 33)
  medium: 0 pass, 19 fail (total: 19)
Arriba filter: 55 rows -> 2 PASS; wrote tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.filter_summary.txt