Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/3d1185e37f7e3dca5b276b88ca25e7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/3d1185e37f7e3dca5b276b88ca25e7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/2a4e2a8bd11f0cc7b6070824174918/tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.tsv
  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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 472
  Pass (FILTER=PASS): 91 (19.3%)
  Fail (FILTER=FAIL): 381 (80.7%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 61
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 47
  confidence_below_min(medium<high): 42
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 39
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 28
  confidence_below_min(low<high): 20
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5

Breakdown by confidence:
  high: 91 pass, 19 fail (total: 110)
  low: 0 pass, 219 fail (total: 219)
  medium: 0 pass, 143 fail (total: 143)
Arriba filter: 472 rows -> 91 PASS; wrote tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.filter_summary.txt