Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/628177ecdffa3b2376ba57b7d765a5/tih_rna_sample_00410_23H5VFLT4_s34.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/e6fab4c3f614e969a1c70df63483c1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/e6fab4c3f614e969a1c70df63483c1/.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-5b456d70-fab3-4fcc-916c-bc437f411fba/48/d36e0303d259ad82d7d96e756f6134/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 151
  Pass (FILTER=PASS): 11 (7.3%)
  Fail (FILTER=FAIL): 140 (92.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(medium<high): 20
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 11 pass, 4 fail (total: 15)
  low: 0 pass, 90 fail (total: 90)
  medium: 0 pass, 46 fail (total: 46)
Arriba filter: 151 rows -> 11 PASS; wrote tih_rna_sample_00410_23H5VFLT4_s34.arriba.fusions.filtered.tsv and tih_rna_sample_00410_23H5VFLT4_s34.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00410_23H5VFLT4_s34.arriba.fusions.filter_summary.txt