Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/7c83017cd14b378e72837b029711f1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/7c83017cd14b378e72837b029711f1/.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/5e/8e5db990dc1d6814978a2190db7c57/tih_rna_sample_00164_B23WHTKLT4_2.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 66
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 66 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(medium<high): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  low: 0 pass, 17 fail (total: 17)
  medium: 0 pass, 49 fail (total: 49)
Arriba filter: 66 rows -> 0 PASS; wrote tih_rna_sample_00164_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00164_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00164_B23WHTKLT4_2.arriba.fusions.filter_summary.txt