Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/b0493d54016009ba3abc565b9c2318/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/b0493d54016009ba3abc565b9c2318/.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/70/f2f30ca21aeb4dd71edd441df8d4de/tih_rna_sample_00166_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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 151
  Pass (FILTER=PASS): 7 (4.6%)
  Fail (FILTER=FAIL): 144 (95.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 7 pass, 2 fail (total: 9)
  low: 0 pass, 66 fail (total: 66)
  medium: 0 pass, 76 fail (total: 76)
Arriba filter: 151 rows -> 7 PASS; wrote tih_rna_sample_00166_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00166_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00166_B23WHTKLT4_2.arriba.fusions.filter_summary.txt