Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/dc27f9f619a134f19fe90edbc04a5b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/dc27f9f619a134f19fe90edbc04a5b/.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/a8/85f0b1e57fc2db4d782f5e1d7e6c65/tih_rna_sample_00480_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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 452
  Pass (FILTER=PASS): 86 (19.0%)
  Fail (FILTER=FAIL): 366 (81.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 61
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 50
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 42
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 33
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 28
  confidence_below_min(low<high): 18
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  total_reads_below_min(6.0<8.0): 4

Breakdown by confidence:
  high: 86 pass, 10 fail (total: 96)
  low: 0 pass, 169 fail (total: 169)
  medium: 0 pass, 187 fail (total: 187)
Arriba filter: 452 rows -> 86 PASS; wrote tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.filter_summary.txt